Internal file for style

logo of company

Where we see the pipeline processes

Author: Adrien Taudière

Date: December 1, 2025

Code 
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/01_bioinformatics.qmd")
source(here::here("R/functions.R"))
Code 
#' ggplot theme for IdEst
#'
#' @description
#' This theme is used by Adrien Taudiere [IdEst](https://adrientaudiere.com/).
#'  Based on [hrbrthemes](https://github.com/hrbrmstr/hrbrthemes/tree/master)
#' `hrbrthemes::theme_ipsum()` by boB Rudis.
#'
#' @param sans_family Font family for sans serif text (default is
#'  "Roboto Condensed" on Windows and "Roboto Condensed Light" on other OS).
#' @param serif_family Font family for serif text (default is "Linux Libertine G").
#' @param mono_family Font family for monospaced text (default is "Fira Code").
#' @param base_size Base font size (default is 11.5).
#' @param plot_title_family Font family for title (default is serif_family).
#' @param plot_title_size Font size for title (default is 18).
#' @param plot_title_face Font face for title (default is "bold").
#' @param plot_title_margin Margin below title (default is 10).
#' @param subtitle_family Font family for subtitle (default is serif_family).
#' @param subtitle_size Font size for subtitle (default is 13).
#' @param subtitle_face Font face for subtitle (default is "plain").
#' @param subtitle_margin Margin below subtitle (default is 15).
#' @param subtitle_color Font color for subtitle (default is "grey30").
#' @param strip_text_family Font family for facet strip text (default is mono_family).
#' @param strip_text_size Font size for facet strip text (default is 13).
#' @param strip_text_face Font face for facet strip text (default is "plain").
#' @param strip_back_grey Logical, whether to use grey background for facet strips
#'   (default is FALSE).
#' @param caption_family Font family for caption (default is sans_family).
#' @param caption_size Font size for caption (default is 9).
#' @param caption_face Font face for caption (default is "plain").
#' @param caption_margin Margin above caption (default is 10).
#' @param axis_text_size Font size for axis text (default is 80\% of base_size).
#' @param axis_text_family  Font family for axis text (default is sans_family).
#' @param axis_title_family Font family for axis titles (default is mono_family).
#' @param axis_title_size Font size for axis titles (default is 12).
#' @param axis_title_face Font face for axis titles (default is "plain").
#' @param axis_title_just Justification for axis titles (default is "c" for center).
#' @param plot_margin Margin around the plot (default is margin(12, 12, 12, 12)).
#' @param panel_spacing Spacing between panels (default is unit(1.2, "lines")).
#' @param grid_col Color for grid lines (default is "#cccccc").
#' @param grid Logical or character, whether to show grid lines (default is TRUE).
#' @param axis_col Color for axis lines (default is "#cccccc").
#' @param axis Logical or character, whether to show axis lines (default is FALSE).
#' @param ticks Logical, whether to show axis ticks (default is FALSE).
#'
#' @return A ggplot2 theme object.
#' @author Adrien Taudiere
#' @export
#'
theme_idest <- function(
  sans_family = if (.Platform$OS.type == "windows") {
    "Roboto Condensed"
  } else {
    "Roboto Condensed Light"
  },
  serif_family = "Linux Libertine G",
  mono_family = "Fira Code",
  base_size = 11.5,
  plot_title_family = serif_family,
  plot_title_size = 18,
  plot_title_face = "bold",
  plot_title_margin = 10,
  subtitle_family = serif_family,
  subtitle_size = 13,
  subtitle_face = "plain",
  subtitle_margin = 15,
  subtitle_color = "grey30",
  strip_text_family = mono_family,
  strip_text_size = 13,
  strip_text_face = "plain",
  strip_back_grey = FALSE,
  caption_family = sans_family,
  caption_size = 9,
  caption_face = "plain",
  caption_margin = 10,
  axis_text_size = base_size * 0.8,
  axis_text_family = sans_family,
  axis_title_family = mono_family,
  axis_title_size = 12,
  axis_title_face = "plain",
  axis_title_just = "c",
  plot_margin = margin(12, 12, 12, 12),
  panel_spacing = grid::unit(1.2, "lines"),
  grid_col = "#cccccc",
  grid = TRUE,
  axis_col = "#cccccc",
  axis = FALSE,
  ticks = FALSE
) {
  ret <- theme_minimal(base_family = sans_family, base_size = base_size)

  ret <- ret + theme(legend.background = element_blank())
  ret <- ret + theme(legend.key = element_blank())

  ret <- ret + theme(plot.margin = plot_margin)
  ret <- ret + theme(panel.spacing = panel_spacing)

  if (inherits(grid, "character") | grid == TRUE) {
    ret <- ret + theme(panel.grid = element_line(color = grid_col, linewidth = 0.2))
    ret <- ret + theme(panel.grid.major = element_line(color = grid_col, linewidth = 0.2))
    ret <- ret + theme(panel.grid.minor = element_line(color = grid_col, linewidth = 0.15))

    if (inherits(grid, "character")) {
      if (regexpr("X", grid)[1] < 0) {
        ret <- ret + theme(panel.grid.major.x = element_blank())
      }
      if (regexpr("Y", grid)[1] < 0) {
        ret <- ret + theme(panel.grid.major.y = element_blank())
      }
      if (regexpr("x", grid)[1] < 0) {
        ret <- ret + theme(panel.grid.minor.x = element_blank())
      }
      if (regexpr("y", grid)[1] < 0) {
        ret <- ret + theme(panel.grid.minor.y = element_blank())
      }
    }
  } else {
    ret <- ret + theme(panel.grid = element_blank())
    ret <- ret + theme(panel.grid.major = element_blank())
    ret <- ret + theme(panel.grid.major.x = element_blank())
    ret <- ret + theme(panel.grid.major.y = element_blank())
    ret <- ret + theme(panel.grid.minor = element_blank())
    ret <- ret + theme(panel.grid.minor.x = element_blank())
    ret <- ret + theme(panel.grid.minor.y = element_blank())
  }

  if (inherits(axis, "character") | axis == TRUE) {
    ret <- ret + theme(axis.line = element_line(color = axis_col, linewidth = 0.15))
    if (inherits(axis, "character")) {
      axis <- tolower(axis)
      if (regexpr("x", axis)[1] < 0) {
        ret <- ret + theme(axis.line.x = element_blank())
      } else {
        ret <- ret + theme(axis.line.x = element_line(color = axis_col, linewidth = 0.15))
      }
      if (regexpr("y", axis)[1] < 0) {
        ret <- ret + theme(axis.line.y = element_blank())
      } else {
        ret <- ret + theme(axis.line.y = element_line(color = axis_col, linewidth = 0.15))
      }
    } else {
      ret <- ret + theme(axis.line.x = element_line(color = axis_col, linewidth = 0.15))
      ret <- ret + theme(axis.line.y = element_line(color = axis_col, linewidth = 0.15))
    }
  } else {
    ret <- ret + theme(axis.line = element_blank())
  }

  if (!ticks) {
    ret <- ret + theme(axis.ticks = element_blank())
    ret <- ret + theme(axis.ticks.x = element_blank())
    ret <- ret + theme(axis.ticks.y = element_blank())
  } else {
    ret <- ret + theme(axis.ticks = element_line(linewidth = 0.15))
    ret <- ret + theme(axis.ticks.x = element_line(linewidth = 0.15))
    ret <- ret + theme(axis.ticks.y = element_line(linewidth = 0.15))
    ret <- ret + theme(axis.ticks.length = grid::unit(5, "pt"))
  }

  xj <- switch(tolower(substr(axis_title_just, 1, 1)),
    b = 0,
    l = 0,
    m = 0.5,
    c = 0.5,
    r = 1,
    t = 1
  )
  yj <- switch(tolower(substr(axis_title_just, 2, 2)),
    b = 0,
    l = 0,
    m = 0.5,
    c = 0.5,
    r = 1,
    t = 1
  )

  ret <- ret + theme(axis.text = element_text(
    size = axis_text_size,
    family = axis_text_family,
    margin = margin(t = 0, r = 0)
  ))
  ret <- ret + theme(axis.text.x = element_text(
    size = axis_text_size,
    family = axis_text_family,
    margin = margin(t = 0)
  ))
  ret <- ret + theme(axis.text.y = element_text(
    size = axis_text_size,
    family = axis_text_family,
    margin = margin(r = 0)
  ))

  ret <- ret + theme(axis.title = element_text(size = axis_title_size, family = axis_title_family))
  ret <- ret + theme(
    axis.title.x = element_text(
      hjust = xj,
      size = axis_title_size,
      family = axis_title_family,
      face = axis_title_face
    )
  )
  ret <- ret + theme(
    axis.title.y = element_text(
      hjust = yj,
      size = axis_title_size,
      family = axis_title_family,
      face = axis_title_face
    )
  )
  ret <- ret + theme(
    axis.title.y.right = element_text(
      hjust = yj,
      size = axis_title_size,
      angle = 90,
      family = axis_title_family,
      face = axis_title_face
    )
  )

  ret <- ret + theme(
    strip.text = element_text(
      hjust = 0,
      size = strip_text_size,
      face = strip_text_face,
      family = strip_text_family
    )
  )

  ret <- ret + theme(
    plot.title = element_text(
      hjust = 0,
      size = plot_title_size,
      margin = margin(b = plot_title_margin),
      family = plot_title_family,
      face = plot_title_face
    )
  )
  ret <- ret + theme(
    plot.subtitle = element_text(
      hjust = 0,
      size = subtitle_size,
      margin = margin(b = subtitle_margin),
      family = subtitle_family,
      face = subtitle_face,
      color = subtitle_color
    )
  )
  ret <- ret + theme(
    plot.caption = element_text(
      hjust = 1,
      size = caption_size,
      margin = margin(t = caption_margin),
      family = caption_family,
      face = caption_face
    )
  )

  if (strip_back_grey) {
    ret <- ret + theme(
      strip.background = element_rect(fill = "grey90", color = NA),
      panel.border = element_rect(color = "grey90", fill = NA)
    )
  }

  ret
}


#' IdEst color palettes
#'
#' @description
#'  Palettes of color for IdEst including also
#'  some palettes from MoMAColors
#'   <https://github.com/BlakeRMills/MoMAColors/blob/main/R/Functions.R>
#'
#'  The available palette are c("all_color_idest", "ligth_color_idest",
#'  "dark_color_idest", "Picabia", "Picasso", "Levine2", "Rattner", "Sidhu",
#'  "Hokusai2", "Hokusai3")
#' @export
#' @author Adrien Taudiere
idest_pal <- list(
  all_color_idest = list(
    c(
      "#dc863b",
      "#faefd1",
      "#2e7891",
      "#8a9da4",
      "#aa4c26",
      "#c8a734",
      "#a6d3e3",
      "#003f5f",
      "#ba63b6",
      "#f20040",
      "#774fa0",
      "#b4dfa7"
    ),
    c(1:11),
    colorblind = FALSE
  ),
  ligth_color_idest = list(
    c("#faefd1", "#a6d3e3", "#b4dfa7", "#8a9da4"),
    c(1:4),
    colorblind = FALSE
  ),
  dark_color_idest = list(
    c(
      "#dc863b",
      "#2e7891",
      "#aa4c26",
      "#c8a734",
      "#003f5f",
      "#ba63b6",
      "#f20040",
      "#774fa0"
    ),
    c(1:8),
    colorblind = FALSE
  ),
  Picabia = list(
    c(
      "#53362e",
      "#744940",
      "#9f7064",
      "#c99582",
      "#e6bcac",
      "#e2d8d6",
      "#a5a6ae",
      "#858794",
      "#666879",
      "#515260",
      "#3d3d47"
    ),
    c(10, 4, 8, 1, 6, 3, 7, 2, 9, 5, 11),
    colorblind = TRUE
  ),
  Picasso = list(
    c(
      "#d5968c",
      "#c2676d",
      "#5c363a",
      "#995041",
      "#45939c",
      "#0f6a81"
    ),
    c(6, 3, 4, 2, 1, 5),
    colorblind = TRUE
  ),
  Levine2 = list(
    c(
      "#E3C1CB",
      "#AD5A6B",
      "#C993A2",
      "#365C83",
      "#384351",
      "#4D8F8B",
      "#CDD6AD"
    ),
    c(7, 1, 5, 3, 6, 2, 4),
    colorblind = TRUE
  ),
  Rattner = list(
    c(
      "#de8e69",
      "#f1be99",
      "#c1bd38",
      "#7a9132",
      "#4c849a",
      "#184363",
      "#5d5686",
      "#a39fc9"
    ),
    c(1, 5, 6, 2, 3, 7, 8, 4),
    colorblind = TRUE
  ),
  Sidhu = list(
    c(
      "#af4646",
      "#762b35",
      "#005187",
      "#251c4a",
      "#78adb7",
      "#4c9a77",
      "#1b7975"
    ),
    c(5, 2, 6, 7, 3, 4, 1),
    colorblind = TRUE
  ),
  Hokusai2 = list(c("#abc9c8", "#72aeb6", "#4692b0", "#2f70a1", "#134b73", "#0a3351"), c(5, 2, 4, 1, 6, 3), colorblind = TRUE), # copy from https://github.com/BlakeRMills/MetBrewer/blob/main/R/PaletteCode.R
  Hokusai3 = list(c("#d8d97a", "#95c36e", "#74c8c3", "#5a97c1", "#295384", "#0a2e57"), c(4, 2, 5, 3, 1, 6), colorblind = TRUE) # copy from https://github.com/BlakeRMills/MetBrewer/blob/main/R/PaletteCode.R
)

#' IdEst continuous color scales for ggplot2
#'
#' @param palette_name The name of the palette to use.
#'  The available palette are c("all_color_idest", "ligth_color_idest",
#'  "dark_color_idest", "Picabia", "Picasso", "Levine2", "Rattner", "Sidhu",
#'  "Hokusai2", "Hokusai3"). See [idest_pal] for more details.
#' @param direction Direction of the palette. 1 for standard, -1 for reversed.
#' @param ... Additional arguments passed to [ggplot2::scale_color_gradientn()].
#'
#' @returns A ggplot2 scale object.
#' @export
#' @author Adrien Taudiere
scale_color_idest_c <- function(palette_name = "all_color_idest", direction = 1, ...) {
  `%notin%` <- Negate(`%in%`)

  if (direction %notin% c(1, -1)) {
    stop("Direction not valid. Please use 1 for standard palette or -1 for reversed palette.")
  }

  scale_color_gradientn(
    colors = idest_colors(
      palette_name = palette_name,
      direction = direction,
      override_order = F
    ),
    ...
  )
}

#' IdEst continuous fill scales for ggplot2
#' @inheritParams scale_color_idest_c
#' @returns A ggplot2 scale object.
#' @export
#' @author Adrien Taudiere
scale_fill_idest_c <- function(palette_name = "all_color_idest", direction = 1, ...) {
  `%notin%` <- Negate(`%in%`)

  if (direction %notin% c(1, -1)) {
    stop("Direction not valid. Please use 1 for standard palette or -1 for reversed palette.")
  }

  scale_color_gradientn(
    colors = idest_colors(
      palette_name = palette_name,
      direction = direction,
      override_order = F
    ),
    ...
  )
}

#' IdEst discrete color scales for ggplot2
#'
#' @param palette_name The name of the palette to use.
#'  The available palette are c("all_color_idest", "ligth_color_idest",
#'  "dark_color_idest", "Picabia", "Picasso", "Levine2", "Rattner", "Sidhu",
#'  "Hokusai2", "Hokusai3"). See [idest_pal] for more details.
#' @param direction Direction of the palette. 1 for standard, -1 for reversed.
#' @param override_order Logical (default FALSE),
#'   whether to override the order of the palette.
#' @param ... Additional arguments passed to [ggplot2::scale_color_gradientn()].
#' @export
#' @returns A ggplot2 scale object.
#' @author Adrien Taudiere
scale_color_idest_d <- function(palette_name = "all_color_idest",
                                direction = 1,
                                override_order = FALSE,
                                ...) {
  discrete_scale(
    aesthetics = "colour",
    scale_name = "moma_d",
    palette = function(n) {
      idest_colors(
        palette_name = palette_name,
        n = n,
        direction = direction,
        override_order = override_order
      )
    },
    ...
  )
}

#' IdEst discrete fill scales for ggplot2
#' @inheritParams scale_color_idest_d
#' @returns A ggplot2 scale object.
#' @export
#' @author Adrien Taudiere
scale_fill_idest_d <- function(palette_name = "all_color_idest",
                               direction = 1,
                               override_order = FALSE,
                               ...) {
  discrete_scale(
    aesthetics = "fill",
    scale_name = "moma_d",
    palette = function(n) {
      idest_colors(
        palette_name = palette_name,
        n = n,
        direction = direction,
        override_order = override_order
      )
    },
    ...
  )
}


#' IdEst colors for ggplot theme_idest
#'
#' @param palette_name The name of the palette to use.
#' The available palette are c("all_color_idest", "ligth_color_idest",
#' "dark_color_idest", "Picabia", "Picasso", "Levine2", "Rattner", "Sidhu",
#' "Hokusai2", "Hokusai3"). See [idest_pal] for more details.
#' @param n Number of colors to return.
#' @param type Type of palette. Either "discrete" or "continuous".
#' @param direction Direction of the palette. 1 for standard, -1 for reversed.
#' @param override_order Logical, whether to override the order of the palette.
#'
#' @returns A vector of colors.
#' @author Adrien Taudiere
#' @export
idest_colors <- function(palette_name = "all_color_idest",
                         n,
                         type = c("discrete", "continuous"),
                         direction = c(1, -1),
                         override_order = FALSE) {
  `%notin%` <- Negate(`%in%`)

  palette <- idest_pal[[palette_name]]

  if (is.null(palette) | is.numeric(palette_name)) {
    stop("Palette does not exist.")
  }

  if (missing(n)) {
    n <- length(palette[[1]])
  }

  if (missing(direction)) {
    direction <- 1
  }

  if (direction %notin% c(1, -1)) {
    stop("Direction not valid. Please use 1 for standard palette or -1 for reversed palette.")
  }

  if (missing(type)) {
    if (n > length(palette[[1]])) {
      type <- "continuous"
    } else {
      type <- "discrete"
    }
  }

  type <- match.arg(type)


  if (type == "discrete" && n > length(palette[[1]])) {
    stop(
      "Number of requested colors greater than what discrete palette can offer, \n use continuous instead."
    )
  }

  continuous <- if (direction == 1) {
    grDevices::colorRampPalette(palette[[1]])(n)
  } else {
    grDevices::colorRampPalette(rev(palette[[1]]))(n)
  }

  discrete <- if (direction == 1 & override_order == FALSE) {
    palette[[1]][which(palette[[2]] %in% c(1:n) == TRUE)]
  } else if (direction == -1 & override_order == FALSE) {
    rev(palette[[1]][which(palette[[2]] %in% c(1:n) == TRUE)])
  } else if (direction == 1 & override_order == TRUE) {
    palette[[1]][1:n]
  } else {
    rev(palette[[1]])[1:n]
  }

  out <- switch(type,
    continuous = continuous,
    discrete = discrete
  )
  structure(out, class = "palette", name = palette_name)
}

Summary of the bioinformatic pipeline

Carbon footprint

Code 
res_ga <- greenAlgoR::ga_targets(store = here::here("_targets/"))
print(paste0(res_ga$carbon_footprint_total_gCO2, " gCO2 equiv. emitted for the whole pipeline"))
#> [1] "185.099466924978 gCO2 equiv. emitted for the whole pipeline"

Timeline and cpu usage

Code 
log_data <- autometric::log_read(
  here::here("data/data_final/autometric_log.txt"),
  units_time = "hours",
  units_memory = "gigabytes"
)

log_data |>
  filter(!grepl("conclude:", phase)) |>
  filter(!grepl("prepare:", phase)) |>
  filter(!grepl("__DEFAULT__", phase)) |>
  ggplot(aes(x = time, y = reorder(phase, desc(time)), color = resident)) +
  geom_line(aes(linewidth = cpu)) +
  scale_color_viridis_b("Memory (Gb)", end = 0.9, direction = -1) +
  theme_idest() +
  xlab("Time (in hours)") +
  ylab("")

Main phyloseq object

You may want to select another targets such as d_asv or d_vs_mumu for example.

Code 
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
Code 
summary_plot_pq(d_pq)

Code 
tar_glimpse(script=here::here("_targets.R"), targets_only = TRUE, callr_arguments = list(show = FALSE))
Code 
tar_meta(store=here::here("_targets/"), targets_only = TRUE) |> 
  dplyr::mutate(time = paste0(seconds %/% 3600,":",seconds %/% 60,":",floor(seconds %% 60)))|>
  dplyr::select(name, seconds, bytes, format, time) |>
  dplyr::mutate(Gb=round(bytes/10^9,2)) |>
  dplyr::arrange(desc(seconds), desc(bytes))  |> 
  kable()


|name                             |   seconds|      bytes|format |time     |   Gb|
|:--------------------------------|---------:|----------:|:------|:--------|----:|
|d_asv                            | 11972.998|    1097339|rds    |3:199:32 | 0.00|
|tax_tab                          |  3971.426|     798938|rds    |1:66:11  | 0.00|
|ddR                              |  2349.852|  141231407|qs     |0:39:9   | 0.14|
|ddF                              |  1053.016|  130244592|qs     |0:17:33  | 0.13|
|filtered                         |   525.178|        154|rds    |0:8:45   | 0.00|
|quality_raw_seq                  |   469.384|      19034|rds    |0:7:49   | 0.00|
|quality_seq_wo_primers           |   469.014|      18891|rds    |0:7:49   | 0.00|
|cutadapt                         |   345.924| 5439202491|file   |0:5:45   | 5.44|
|quality_seq_filtered_trimmed_REV |   236.071|      11304|rds    |0:3:56   | 0.00|
|quality_seq_filtered_trimmed_FW  |   230.575|      11304|rds    |0:3:50   | 0.00|
|derep_rs                         |   179.230| 2678399208|qs     |0:2:59   | 2.68|
|err_rs                           |   170.105|      24428|qs     |0:2:50   | 0.00|
|derep_fs                         |   169.472| 1681165403|qs     |0:2:49   | 1.68|
|err_fs                           |   163.737|      21602|qs     |0:2:43   | 0.00|
|track_sequences_samples_clusters |   103.993|        443|rds    |0:1:43   | 0.00|
|merged_seq                       |   100.951|    1408727|qs     |0:1:40   | 0.00|
|track_by_samples                 |    99.281|       8932|rds    |0:1:39   | 0.00|
|seqtab_wo_chimera                |    14.227|     805785|rds    |0:0:14   | 0.00|
|bioinfo_report                   |    10.633|          0|rds    |0:0:10   | 0.00|
|d_vs_mumu                        |     5.841|     889413|rds    |0:0:5    | 0.00|
|d_vs                             |     4.078|     902883|rds    |0:0:4    | 0.00|
|d_vs_mumu_rarefy                 |     0.770|     856846|rds    |0:0:0    | 0.00|
|seq_tab_Pairs                    |     0.171|     957602|rds    |0:0:0    | 0.00|
|data_phyloseq                    |     0.105|    1026818|rds    |0:0:0    | 0.00|
|s_d                              |     0.060|      12331|rds    |0:0:0    | 0.00|
|data_raw                         |     0.026|       5224|rds    |0:0:0    | 0.00|
|seqtab                           |     0.010|     798807|rds    |0:0:0    | 0.00|
|asv_tab                          |     0.010|     798670|rds    |0:0:0    | 0.00|
|sam_tab                          |     0.004|       6974|rds    |0:0:0    | 0.00|
|file_sam_data_csv                |     0.002|      24577|file   |0:0:0    | 0.00|
|fastq_files_folder               |     0.001| 6578858328|file   |0:0:0    | 6.58|
|file_refseq_taxo                 |     0.001|   72883169|file   |0:0:0    | 0.07|
|samp_n_otu_table                 |     0.001|       1974|rds    |0:0:0    | 0.00|
|data_fnfs                        |     0.000|       2675|rds    |0:0:0    | 0.00|
|data_fnrs                        |     0.000|       2675|rds    |0:0:0    | 0.00|

Load phyloseq object from targets store

Code 
d_pq <- tar_read("d_vs", store=here::here("_targets/"))

The {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.

The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.

Sample data

Code 
DT::datatable(d_pq@sam_data)

Sequences, samples and clusters across the pipeline

Code 
kable(tar_read(track_sequences_samples_clusters, store=here::here("_targets/")))


|                                                       | nb_sequences| nb_clusters| nb_samples|
|:------------------------------------------------------|------------:|-----------:|----------:|
|Raw Forward sequences                                  |     15651813|          NA|        375|
|Forward wo primers                                     |     15358185|          NA|        375|
|Forward sequences                                      |     14080888|       29767|        359|
|Paired sequences                                       |      9858255|       12427|        359|
|Paired sequences without chimera                       |      9521256|       10314|        359|
|Paired sequences without chimera and longer than 200bp |      9486698|       10154|        359|
|ASV denoising                                          |      9457849|       10154|        358|
|OTU after vsearch reclustering at 97%                  |      9457849|        4483|        358|
|OTU vs after mumu cleaning algorithm                   |      9457849|        4132|        332|
|OTU vs + mumu + rarefaction by sequencing depth        |       590000|        3541|        295|
Code 
tab_samp <- tar_read(track_by_samples, store=here::here("_targets/"))

for (li in names(tab_samp)) {
  print(knitr::kable(tab_samp[[li]], caption = li, format="html"))
  cat('\n<!-- -->\n\n')
}
samp_0-18_S112
nb_sequences nb_clusters nb_samples
ASV denoising 32638 82 1
OTU after vsearch reclustering at 97% 32638 56 1
OTU vs after mumu cleaning algorithm 32638 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_0-34_S180
nb_sequences nb_clusters nb_samples
ASV denoising 32800 142 1
OTU after vsearch reclustering at 97% 32800 128 1
OTU vs after mumu cleaning algorithm 32800 119 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_0-50_S190
nb_sequences nb_clusters nb_samples
ASV denoising 30887 94 1
OTU after vsearch reclustering at 97% 30887 84 1
OTU vs after mumu cleaning algorithm 30887 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_001A_S145
nb_sequences nb_clusters nb_samples
ASV denoising 32509 133 1
OTU after vsearch reclustering at 97% 32509 115 1
OTU vs after mumu cleaning algorithm 32509 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_001B_S170
nb_sequences nb_clusters nb_samples
ASV denoising 44333 49 1
OTU after vsearch reclustering at 97% 44333 38 1
OTU vs after mumu cleaning algorithm 44333 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_001C_S98
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_002A_S104
nb_sequences nb_clusters nb_samples
ASV denoising 20014 50 1
OTU after vsearch reclustering at 97% 20014 41 1
OTU vs after mumu cleaning algorithm 20014 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_002B_S160
nb_sequences nb_clusters nb_samples
ASV denoising 34676 75 1
OTU after vsearch reclustering at 97% 34676 65 1
OTU vs after mumu cleaning algorithm 34676 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_002C_S139
nb_sequences nb_clusters nb_samples
ASV denoising 43787 115 1
OTU after vsearch reclustering at 97% 43787 98 1
OTU vs after mumu cleaning algorithm 43787 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 69 1
samp_003A_S115
nb_sequences nb_clusters nb_samples
ASV denoising 29108 84 1
OTU after vsearch reclustering at 97% 29108 65 1
OTU vs after mumu cleaning algorithm 29108 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_003C_S182
nb_sequences nb_clusters nb_samples
ASV denoising 32794 103 1
OTU after vsearch reclustering at 97% 32794 87 1
OTU vs after mumu cleaning algorithm 32794 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_004A_S167
nb_sequences nb_clusters nb_samples
ASV denoising 38461 60 1
OTU after vsearch reclustering at 97% 38461 39 1
OTU vs after mumu cleaning algorithm 38461 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_004B_S148
nb_sequences nb_clusters nb_samples
ASV denoising 30435 57 1
OTU after vsearch reclustering at 97% 30435 39 1
OTU vs after mumu cleaning algorithm 30435 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_004C_S138
nb_sequences nb_clusters nb_samples
ASV denoising 38056 92 1
OTU after vsearch reclustering at 97% 38056 73 1
OTU vs after mumu cleaning algorithm 38056 73 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_005A_S111
nb_sequences nb_clusters nb_samples
ASV denoising 35930 102 1
OTU after vsearch reclustering at 97% 35930 91 1
OTU vs after mumu cleaning algorithm 35930 82 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_005B_S200
nb_sequences nb_clusters nb_samples
ASV denoising 26521 67 1
OTU after vsearch reclustering at 97% 26521 58 1
OTU vs after mumu cleaning algorithm 26521 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_005C_S178
nb_sequences nb_clusters nb_samples
ASV denoising 36188 106 1
OTU after vsearch reclustering at 97% 36188 84 1
OTU vs after mumu cleaning algorithm 36188 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_006A_S128
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_006B_S116
nb_sequences nb_clusters nb_samples
ASV denoising 27642 166 1
OTU after vsearch reclustering at 97% 27642 149 1
OTU vs after mumu cleaning algorithm 27642 147 1
OTU vs + mumu + rarefaction by sequencing depth 2000 129 1
samp_006C_S156
nb_sequences nb_clusters nb_samples
ASV denoising 73 2 1
OTU after vsearch reclustering at 97% 73 2 1
OTU vs after mumu cleaning algorithm 73 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_007A_S130
nb_sequences nb_clusters nb_samples
ASV denoising 39116 63 1
OTU after vsearch reclustering at 97% 39116 49 1
OTU vs after mumu cleaning algorithm 39116 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_007B_S191
nb_sequences nb_clusters nb_samples
ASV denoising 33534 126 1
OTU after vsearch reclustering at 97% 33534 113 1
OTU vs after mumu cleaning algorithm 33534 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_007C_S131
nb_sequences nb_clusters nb_samples
ASV denoising 39127 80 1
OTU after vsearch reclustering at 97% 39127 65 1
OTU vs after mumu cleaning algorithm 39127 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_008A_S153
nb_sequences nb_clusters nb_samples
ASV denoising 42480 74 1
OTU after vsearch reclustering at 97% 42480 45 1
OTU vs after mumu cleaning algorithm 42480 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_008A-PL2_S133
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_008C_S113
nb_sequences nb_clusters nb_samples
ASV denoising 28651 89 1
OTU after vsearch reclustering at 97% 28651 80 1
OTU vs after mumu cleaning algorithm 28651 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_009A_S134
nb_sequences nb_clusters nb_samples
ASV denoising 37517 120 1
OTU after vsearch reclustering at 97% 37517 103 1
OTU vs after mumu cleaning algorithm 37517 102 1
OTU vs + mumu + rarefaction by sequencing depth 2000 85 1
samp_009B_S174
nb_sequences nb_clusters nb_samples
ASV denoising 478 3 1
OTU after vsearch reclustering at 97% 478 3 1
OTU vs after mumu cleaning algorithm 478 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_009B-PL2_S109
nb_sequences nb_clusters nb_samples
ASV denoising 32968 123 1
OTU after vsearch reclustering at 97% 32968 104 1
OTU vs after mumu cleaning algorithm 32968 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 92 1
samp_009C_S105
nb_sequences nb_clusters nb_samples
ASV denoising 32 1 1
OTU after vsearch reclustering at 97% 32 1 1
OTU vs after mumu cleaning algorithm 32 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_010A_S189
nb_sequences nb_clusters nb_samples
ASV denoising 33028 115 1
OTU after vsearch reclustering at 97% 33028 91 1
OTU vs after mumu cleaning algorithm 33028 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_010B_S185
nb_sequences nb_clusters nb_samples
ASV denoising 33175 106 1
OTU after vsearch reclustering at 97% 33175 74 1
OTU vs after mumu cleaning algorithm 33175 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_010C_S197
nb_sequences nb_clusters nb_samples
ASV denoising 26265 79 1
OTU after vsearch reclustering at 97% 26265 73 1
OTU vs after mumu cleaning algorithm 26265 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_011A_S123
nb_sequences nb_clusters nb_samples
ASV denoising 47924 66 1
OTU after vsearch reclustering at 97% 47924 60 1
OTU vs after mumu cleaning algorithm 47924 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_011B_S121
nb_sequences nb_clusters nb_samples
ASV denoising 21388 70 1
OTU after vsearch reclustering at 97% 21388 58 1
OTU vs after mumu cleaning algorithm 21388 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_011C-PL2_S172
nb_sequences nb_clusters nb_samples
ASV denoising 31892 9 1
OTU after vsearch reclustering at 97% 31892 6 1
OTU vs after mumu cleaning algorithm 31892 6 1
OTU vs + mumu + rarefaction by sequencing depth 2000 6 1
samp_012A_S173
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_012B_S141
nb_sequences nb_clusters nb_samples
ASV denoising 31818 146 1
OTU after vsearch reclustering at 97% 31818 116 1
OTU vs after mumu cleaning algorithm 31818 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_012C_S126
nb_sequences nb_clusters nb_samples
ASV denoising 37039 59 1
OTU after vsearch reclustering at 97% 37039 53 1
OTU vs after mumu cleaning algorithm 37039 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_013A_S163
nb_sequences nb_clusters nb_samples
ASV denoising 32984 137 1
OTU after vsearch reclustering at 97% 32984 117 1
OTU vs after mumu cleaning algorithm 32984 115 1
OTU vs + mumu + rarefaction by sequencing depth 2000 102 1
samp_013B_S188
nb_sequences nb_clusters nb_samples
ASV denoising 41508 161 1
OTU after vsearch reclustering at 97% 41508 127 1
OTU vs after mumu cleaning algorithm 41508 122 1
OTU vs + mumu + rarefaction by sequencing depth 2000 102 1
samp_013D_S194
nb_sequences nb_clusters nb_samples
ASV denoising 27707 80 1
OTU after vsearch reclustering at 97% 27707 71 1
OTU vs after mumu cleaning algorithm 27707 71 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_014A_S196
nb_sequences nb_clusters nb_samples
ASV denoising 18037 88 1
OTU after vsearch reclustering at 97% 18037 85 1
OTU vs after mumu cleaning algorithm 18037 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_014B_S154
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_014C_S114
nb_sequences nb_clusters nb_samples
ASV denoising 52044 86 1
OTU after vsearch reclustering at 97% 52044 70 1
OTU vs after mumu cleaning algorithm 52044 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_015A_S146
nb_sequences nb_clusters nb_samples
ASV denoising 34880 90 1
OTU after vsearch reclustering at 97% 34880 78 1
OTU vs after mumu cleaning algorithm 34880 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 63 1
samp_015C_S103
nb_sequences nb_clusters nb_samples
ASV denoising 33135 138 1
OTU after vsearch reclustering at 97% 33135 116 1
OTU vs after mumu cleaning algorithm 33135 116 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_016A_S119
nb_sequences nb_clusters nb_samples
ASV denoising 35616 138 1
OTU after vsearch reclustering at 97% 35616 127 1
OTU vs after mumu cleaning algorithm 35616 125 1
OTU vs + mumu + rarefaction by sequencing depth 2000 105 1
samp_016B_S176
nb_sequences nb_clusters nb_samples
ASV denoising 15084 85 1
OTU after vsearch reclustering at 97% 15084 75 1
OTU vs after mumu cleaning algorithm 15084 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_017A_S285
nb_sequences nb_clusters nb_samples
ASV denoising 20297 134 1
OTU after vsearch reclustering at 97% 20297 122 1
OTU vs after mumu cleaning algorithm 20297 118 1
OTU vs + mumu + rarefaction by sequencing depth 2000 109 1
samp_017B_S283
nb_sequences nb_clusters nb_samples
ASV denoising 28977 106 1
OTU after vsearch reclustering at 97% 28977 86 1
OTU vs after mumu cleaning algorithm 28977 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 74 1
samp_017C-PL2_S183
nb_sequences nb_clusters nb_samples
ASV denoising 30285 162 1
OTU after vsearch reclustering at 97% 30285 131 1
OTU vs after mumu cleaning algorithm 30285 121 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_025A_S118
nb_sequences nb_clusters nb_samples
ASV denoising 19459 93 1
OTU after vsearch reclustering at 97% 19459 85 1
OTU vs after mumu cleaning algorithm 19459 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_037A_S151
nb_sequences nb_clusters nb_samples
ASV denoising 31 1 1
OTU after vsearch reclustering at 97% 31 1 1
OTU vs after mumu cleaning algorithm 31 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_11Aa_S265
nb_sequences nb_clusters nb_samples
ASV denoising 26320 89 1
OTU after vsearch reclustering at 97% 26320 83 1
OTU vs after mumu cleaning algorithm 26320 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_11Ab_S269
nb_sequences nb_clusters nb_samples
ASV denoising 24639 101 1
OTU after vsearch reclustering at 97% 24639 98 1
OTU vs after mumu cleaning algorithm 24639 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_11Ba_S291
nb_sequences nb_clusters nb_samples
ASV denoising 14794 69 1
OTU after vsearch reclustering at 97% 14794 58 1
OTU vs after mumu cleaning algorithm 14794 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_11Bb_S306
nb_sequences nb_clusters nb_samples
ASV denoising 8631 34 1
OTU after vsearch reclustering at 97% 8631 27 1
OTU vs after mumu cleaning algorithm 8631 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_11Ca_S272
nb_sequences nb_clusters nb_samples
ASV denoising 21061 109 1
OTU after vsearch reclustering at 97% 21061 105 1
OTU vs after mumu cleaning algorithm 21061 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_11Cb_S217
nb_sequences nb_clusters nb_samples
ASV denoising 20468 112 1
OTU after vsearch reclustering at 97% 20468 104 1
OTU vs after mumu cleaning algorithm 20468 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_11D_S62
nb_sequences nb_clusters nb_samples
ASV denoising 38792 138 1
OTU after vsearch reclustering at 97% 38792 120 1
OTU vs after mumu cleaning algorithm 38792 119 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_11Da_S300
nb_sequences nb_clusters nb_samples
ASV denoising 32604 149 1
OTU after vsearch reclustering at 97% 32604 131 1
OTU vs after mumu cleaning algorithm 32604 129 1
OTU vs + mumu + rarefaction by sequencing depth 2000 104 1
samp_11Da-PL4_S292
nb_sequences nb_clusters nb_samples
ASV denoising 30807 130 1
OTU after vsearch reclustering at 97% 30807 114 1
OTU vs after mumu cleaning algorithm 30807 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_11E_S19
nb_sequences nb_clusters nb_samples
ASV denoising 40656 148 1
OTU after vsearch reclustering at 97% 40656 124 1
OTU vs after mumu cleaning algorithm 40656 124 1
OTU vs + mumu + rarefaction by sequencing depth 2000 103 1
samp_11Ea_S232
nb_sequences nb_clusters nb_samples
ASV denoising 33209 151 1
OTU after vsearch reclustering at 97% 33209 130 1
OTU vs after mumu cleaning algorithm 33209 129 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_11Eb_S207
nb_sequences nb_clusters nb_samples
ASV denoising 25660 149 1
OTU after vsearch reclustering at 97% 25660 134 1
OTU vs after mumu cleaning algorithm 25660 133 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_11F_S54
nb_sequences nb_clusters nb_samples
ASV denoising 39358 81 1
OTU after vsearch reclustering at 97% 39358 69 1
OTU vs after mumu cleaning algorithm 39358 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_11Fa_S259
nb_sequences nb_clusters nb_samples
ASV denoising 27965 69 1
OTU after vsearch reclustering at 97% 27965 60 1
OTU vs after mumu cleaning algorithm 27965 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_11G_S32
nb_sequences nb_clusters nb_samples
ASV denoising 44134 81 1
OTU after vsearch reclustering at 97% 44134 67 1
OTU vs after mumu cleaning algorithm 44134 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_11Ga_S237
nb_sequences nb_clusters nb_samples
ASV denoising 40286 96 1
OTU after vsearch reclustering at 97% 40286 73 1
OTU vs after mumu cleaning algorithm 40286 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_11Gb_S236
nb_sequences nb_clusters nb_samples
ASV denoising 36217 85 1
OTU after vsearch reclustering at 97% 36217 67 1
OTU vs after mumu cleaning algorithm 36217 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_11H_S93
nb_sequences nb_clusters nb_samples
ASV denoising 41219 94 1
OTU after vsearch reclustering at 97% 41219 89 1
OTU vs after mumu cleaning algorithm 41219 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_11Ha_S310
nb_sequences nb_clusters nb_samples
ASV denoising 31275 81 1
OTU after vsearch reclustering at 97% 31275 78 1
OTU vs after mumu cleaning algorithm 31275 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_11Hb_S198
nb_sequences nb_clusters nb_samples
ASV denoising 28316 120 1
OTU after vsearch reclustering at 97% 28316 112 1
OTU vs after mumu cleaning algorithm 28316 111 1
OTU vs + mumu + rarefaction by sequencing depth 2000 91 1
samp_11I_S166
nb_sequences nb_clusters nb_samples
ASV denoising 33951 85 1
OTU after vsearch reclustering at 97% 33951 63 1
OTU vs after mumu cleaning algorithm 33951 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_11Ia_S222
nb_sequences nb_clusters nb_samples
ASV denoising 22942 61 1
OTU after vsearch reclustering at 97% 22942 48 1
OTU vs after mumu cleaning algorithm 22942 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_11Ib_S225
nb_sequences nb_clusters nb_samples
ASV denoising 36015 83 1
OTU after vsearch reclustering at 97% 36015 59 1
OTU vs after mumu cleaning algorithm 36015 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_15B_S140
nb_sequences nb_clusters nb_samples
ASV denoising 19292 113 1
OTU after vsearch reclustering at 97% 19292 96 1
OTU vs after mumu cleaning algorithm 19292 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_16C_S168
nb_sequences nb_clusters nb_samples
ASV denoising 33979 123 1
OTU after vsearch reclustering at 97% 33979 100 1
OTU vs after mumu cleaning algorithm 33979 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_20A_S144
nb_sequences nb_clusters nb_samples
ASV denoising 31651 136 1
OTU after vsearch reclustering at 97% 31651 116 1
OTU vs after mumu cleaning algorithm 31651 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 92 1
samp_20Aa_S249
nb_sequences nb_clusters nb_samples
ASV denoising 27873 130 1
OTU after vsearch reclustering at 97% 27873 116 1
OTU vs after mumu cleaning algorithm 27873 114 1
OTU vs + mumu + rarefaction by sequencing depth 2000 100 1
samp_20Ab_S252
nb_sequences nb_clusters nb_samples
ASV denoising 42903 161 1
OTU after vsearch reclustering at 97% 42903 133 1
OTU vs after mumu cleaning algorithm 42903 125 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_20Ab-PL3_S241
nb_sequences nb_clusters nb_samples
ASV denoising 29548 70 1
OTU after vsearch reclustering at 97% 29548 43 1
OTU vs after mumu cleaning algorithm 29548 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_20B_S102
nb_sequences nb_clusters nb_samples
ASV denoising 30453 102 1
OTU after vsearch reclustering at 97% 30453 89 1
OTU vs after mumu cleaning algorithm 30453 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 78 1
samp_20Ba_S278
nb_sequences nb_clusters nb_samples
ASV denoising 28491 89 1
OTU after vsearch reclustering at 97% 28491 81 1
OTU vs after mumu cleaning algorithm 28491 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_20Bb_S277
nb_sequences nb_clusters nb_samples
ASV denoising 25862 96 1
OTU after vsearch reclustering at 97% 25862 87 1
OTU vs after mumu cleaning algorithm 25862 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_20C_S49
nb_sequences nb_clusters nb_samples
ASV denoising 49496 120 1
OTU after vsearch reclustering at 97% 49496 100 1
OTU vs after mumu cleaning algorithm 49496 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_20Ca_S319
nb_sequences nb_clusters nb_samples
ASV denoising 27 1 1
OTU after vsearch reclustering at 97% 27 1 1
OTU vs after mumu cleaning algorithm 27 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Cb_S303
nb_sequences nb_clusters nb_samples
ASV denoising 38864 72 1
OTU after vsearch reclustering at 97% 38864 70 1
OTU vs after mumu cleaning algorithm 38864 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_20D_S82
nb_sequences nb_clusters nb_samples
ASV denoising 40939 159 1
OTU after vsearch reclustering at 97% 40939 132 1
OTU vs after mumu cleaning algorithm 40939 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 108 1
samp_20Da_S238
nb_sequences nb_clusters nb_samples
ASV denoising 1405 9 1
OTU after vsearch reclustering at 97% 1405 8 1
OTU vs after mumu cleaning algorithm 1405 8 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20E_S181
nb_sequences nb_clusters nb_samples
ASV denoising 37745 130 1
OTU after vsearch reclustering at 97% 37745 105 1
OTU vs after mumu cleaning algorithm 37745 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_20Ea_S251
nb_sequences nb_clusters nb_samples
ASV denoising 31599 164 1
OTU after vsearch reclustering at 97% 31599 147 1
OTU vs after mumu cleaning algorithm 31599 143 1
OTU vs + mumu + rarefaction by sequencing depth 2000 125 1
samp_20Eb_S294
nb_sequences nb_clusters nb_samples
ASV denoising 27159 130 1
OTU after vsearch reclustering at 97% 27159 114 1
OTU vs after mumu cleaning algorithm 27159 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 100 1
samp_20F_S143
nb_sequences nb_clusters nb_samples
ASV denoising 35072 152 1
OTU after vsearch reclustering at 97% 35072 131 1
OTU vs after mumu cleaning algorithm 35072 129 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_20Fb_S214
nb_sequences nb_clusters nb_samples
ASV denoising 54 1 1
OTU after vsearch reclustering at 97% 54 1 1
OTU vs after mumu cleaning algorithm 54 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20G_S132
nb_sequences nb_clusters nb_samples
ASV denoising 38558 107 1
OTU after vsearch reclustering at 97% 38558 69 1
OTU vs after mumu cleaning algorithm 38558 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_20Ga_S220
nb_sequences nb_clusters nb_samples
ASV denoising 159 4 1
OTU after vsearch reclustering at 97% 159 4 1
OTU vs after mumu cleaning algorithm 159 4 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Ga2_S239
nb_sequences nb_clusters nb_samples
ASV denoising 26246 65 1
OTU after vsearch reclustering at 97% 26246 55 1
OTU vs after mumu cleaning algorithm 26246 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_20Gb_S284
nb_sequences nb_clusters nb_samples
ASV denoising 24283 96 1
OTU after vsearch reclustering at 97% 24283 73 1
OTU vs after mumu cleaning algorithm 24283 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_20H_S45
nb_sequences nb_clusters nb_samples
ASV denoising 43290 123 1
OTU after vsearch reclustering at 97% 43290 85 1
OTU vs after mumu cleaning algorithm 43290 85 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_20Ha_S219
nb_sequences nb_clusters nb_samples
ASV denoising 148 11 1
OTU after vsearch reclustering at 97% 148 11 1
OTU vs after mumu cleaning algorithm 148 11 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_20Hb_S230
nb_sequences nb_clusters nb_samples
ASV denoising 34057 143 1
OTU after vsearch reclustering at 97% 34057 107 1
OTU vs after mumu cleaning algorithm 34057 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_20I_S192
nb_sequences nb_clusters nb_samples
ASV denoising 39159 71 1
OTU after vsearch reclustering at 97% 39159 42 1
OTU vs after mumu cleaning algorithm 39159 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_20Ia_S224
nb_sequences nb_clusters nb_samples
ASV denoising 2197 10 1
OTU after vsearch reclustering at 97% 2197 9 1
OTU vs after mumu cleaning algorithm 2197 9 1
OTU vs + mumu + rarefaction by sequencing depth 2000 9 1
samp_20Ib_S289
nb_sequences nb_clusters nb_samples
ASV denoising 29987 63 1
OTU after vsearch reclustering at 97% 29987 35 1
OTU vs after mumu cleaning algorithm 29987 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_21A_S94
nb_sequences nb_clusters nb_samples
ASV denoising 35855 107 1
OTU after vsearch reclustering at 97% 35855 65 1
OTU vs after mumu cleaning algorithm 35855 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_21B_S7
nb_sequences nb_clusters nb_samples
ASV denoising 38573 79 1
OTU after vsearch reclustering at 97% 38573 58 1
OTU vs after mumu cleaning algorithm 38573 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_21Bb_S282
nb_sequences nb_clusters nb_samples
ASV denoising 28037 59 1
OTU after vsearch reclustering at 97% 28037 48 1
OTU vs after mumu cleaning algorithm 28037 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_21C_S77
nb_sequences nb_clusters nb_samples
ASV denoising 27592 120 1
OTU after vsearch reclustering at 97% 27592 117 1
OTU vs after mumu cleaning algorithm 27592 117 1
OTU vs + mumu + rarefaction by sequencing depth 2000 105 1
samp_21Ca_S246
nb_sequences nb_clusters nb_samples
ASV denoising 33801 144 1
OTU after vsearch reclustering at 97% 33801 134 1
OTU vs after mumu cleaning algorithm 33801 129 1
OTU vs + mumu + rarefaction by sequencing depth 2000 109 1
samp_21Cb_S276
nb_sequences nb_clusters nb_samples
ASV denoising 28543 125 1
OTU after vsearch reclustering at 97% 28543 115 1
OTU vs after mumu cleaning algorithm 28543 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_21D_S44
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21E_S47
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21eEb_S258
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21F_S48
nb_sequences nb_clusters nb_samples
ASV denoising 44927 14 1
OTU after vsearch reclustering at 97% 44927 10 1
OTU vs after mumu cleaning algorithm 44927 10 1
OTU vs + mumu + rarefaction by sequencing depth 2000 10 1
samp_21Fa_S253
nb_sequences nb_clusters nb_samples
ASV denoising 292 9 1
OTU after vsearch reclustering at 97% 292 9 1
OTU vs after mumu cleaning algorithm 292 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21G_S38
nb_sequences nb_clusters nb_samples
ASV denoising 32535 27 1
OTU after vsearch reclustering at 97% 32535 17 1
OTU vs after mumu cleaning algorithm 32535 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 16 1
samp_21Ga_S290
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_21Gb_S296
nb_sequences nb_clusters nb_samples
ASV denoising 30146 26 1
OTU after vsearch reclustering at 97% 30146 15 1
OTU vs after mumu cleaning algorithm 30146 15 1
OTU vs + mumu + rarefaction by sequencing depth 2000 14 1
samp_21H_S68
nb_sequences nb_clusters nb_samples
ASV denoising 24269 69 1
OTU after vsearch reclustering at 97% 24269 63 1
OTU vs after mumu cleaning algorithm 24269 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_21Ha_S321
nb_sequences nb_clusters nb_samples
ASV denoising 28512 18 1
OTU after vsearch reclustering at 97% 28512 14 1
OTU vs after mumu cleaning algorithm 28512 14 1
OTU vs + mumu + rarefaction by sequencing depth 2000 14 1
samp_21HD_S195
nb_sequences nb_clusters nb_samples
ASV denoising 24741 74 1
OTU after vsearch reclustering at 97% 24741 70 1
OTU vs after mumu cleaning algorithm 24741 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_21I_S50
nb_sequences nb_clusters nb_samples
ASV denoising 39333 67 1
OTU after vsearch reclustering at 97% 39333 51 1
OTU vs after mumu cleaning algorithm 39333 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_21Ia_S233
nb_sequences nb_clusters nb_samples
ASV denoising 28102 64 1
OTU after vsearch reclustering at 97% 28102 55 1
OTU vs after mumu cleaning algorithm 28102 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_21Ib_S271
nb_sequences nb_clusters nb_samples
ASV denoising 28174 63 1
OTU after vsearch reclustering at 97% 28174 55 1
OTU vs after mumu cleaning algorithm 28174 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_22A_S15
nb_sequences nb_clusters nb_samples
ASV denoising 33762 120 1
OTU after vsearch reclustering at 97% 33762 90 1
OTU vs after mumu cleaning algorithm 33762 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_22D_S87
nb_sequences nb_clusters nb_samples
ASV denoising 30082 72 1
OTU after vsearch reclustering at 97% 30082 70 1
OTU vs after mumu cleaning algorithm 30082 69 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_22E_S73
nb_sequences nb_clusters nb_samples
ASV denoising 40930 71 1
OTU after vsearch reclustering at 97% 40930 52 1
OTU vs after mumu cleaning algorithm 40930 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_22F_S60
nb_sequences nb_clusters nb_samples
ASV denoising 39874 131 1
OTU after vsearch reclustering at 97% 39874 117 1
OTU vs after mumu cleaning algorithm 39874 111 1
OTU vs + mumu + rarefaction by sequencing depth 2000 92 1
samp_23C_S84
nb_sequences nb_clusters nb_samples
ASV denoising 44609 146 1
OTU after vsearch reclustering at 97% 44609 135 1
OTU vs after mumu cleaning algorithm 44609 133 1
OTU vs + mumu + rarefaction by sequencing depth 2000 103 1
samp_25B_S52
nb_sequences nb_clusters nb_samples
ASV denoising 37795 157 1
OTU after vsearch reclustering at 97% 37795 125 1
OTU vs after mumu cleaning algorithm 37795 122 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1
samp_25C_S74
nb_sequences nb_clusters nb_samples
ASV denoising 48235 125 1
OTU after vsearch reclustering at 97% 48235 115 1
OTU vs after mumu cleaning algorithm 48235 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_25D_S76
nb_sequences nb_clusters nb_samples
ASV denoising 31545 55 1
OTU after vsearch reclustering at 97% 31545 44 1
OTU vs after mumu cleaning algorithm 31545 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_25E_S81
nb_sequences nb_clusters nb_samples
ASV denoising 25525 122 1
OTU after vsearch reclustering at 97% 25525 107 1
OTU vs after mumu cleaning algorithm 25525 102 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_25F_S67
nb_sequences nb_clusters nb_samples
ASV denoising 21 1 1
OTU after vsearch reclustering at 97% 21 1 1
OTU vs after mumu cleaning algorithm 21 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_26A_S83
nb_sequences nb_clusters nb_samples
ASV denoising 3826 45 1
OTU after vsearch reclustering at 97% 3826 45 1
OTU vs after mumu cleaning algorithm 3826 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_26B_S65
nb_sequences nb_clusters nb_samples
ASV denoising 37760 51 1
OTU after vsearch reclustering at 97% 37760 38 1
OTU vs after mumu cleaning algorithm 37760 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_26C_S8
nb_sequences nb_clusters nb_samples
ASV denoising 39396 63 1
OTU after vsearch reclustering at 97% 39396 41 1
OTU vs after mumu cleaning algorithm 39396 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_26D_S80
nb_sequences nb_clusters nb_samples
ASV denoising 37203 48 1
OTU after vsearch reclustering at 97% 37203 38 1
OTU vs after mumu cleaning algorithm 37203 37 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_26E_S135
nb_sequences nb_clusters nb_samples
ASV denoising 772 17 1
OTU after vsearch reclustering at 97% 772 17 1
OTU vs after mumu cleaning algorithm 772 17 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_26F_S66
nb_sequences nb_clusters nb_samples
ASV denoising 38177 59 1
OTU after vsearch reclustering at 97% 38177 41 1
OTU vs after mumu cleaning algorithm 38177 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_27A_S24
nb_sequences nb_clusters nb_samples
ASV denoising 38594 134 1
OTU after vsearch reclustering at 97% 38594 111 1
OTU vs after mumu cleaning algorithm 38594 110 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_27Aa_S235
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Ab_S293
nb_sequences nb_clusters nb_samples
ASV denoising 30071 155 1
OTU after vsearch reclustering at 97% 30071 138 1
OTU vs after mumu cleaning algorithm 30071 136 1
OTU vs + mumu + rarefaction by sequencing depth 2000 118 1
samp_27B_S17
nb_sequences nb_clusters nb_samples
ASV denoising 55777 70 1
OTU after vsearch reclustering at 97% 55777 45 1
OTU vs after mumu cleaning algorithm 55777 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_27Ba_S221
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Bb_S298
nb_sequences nb_clusters nb_samples
ASV denoising 29089 47 1
OTU after vsearch reclustering at 97% 29089 39 1
OTU vs after mumu cleaning algorithm 29089 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_27C_S53
nb_sequences nb_clusters nb_samples
ASV denoising 21045 85 1
OTU after vsearch reclustering at 97% 21045 69 1
OTU vs after mumu cleaning algorithm 21045 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_27Ca_S267
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Cb_S299
nb_sequences nb_clusters nb_samples
ASV denoising 1382 32 1
OTU after vsearch reclustering at 97% 1382 29 1
OTU vs after mumu cleaning algorithm 1382 27 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27D_S35
nb_sequences nb_clusters nb_samples
ASV denoising 63807 82 1
OTU after vsearch reclustering at 97% 63807 60 1
OTU vs after mumu cleaning algorithm 63807 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_27Db_S311
nb_sequences nb_clusters nb_samples
ASV denoising 35936 78 1
OTU after vsearch reclustering at 97% 35936 67 1
OTU vs after mumu cleaning algorithm 35936 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_27E_S89
nb_sequences nb_clusters nb_samples
ASV denoising 37957 129 1
OTU after vsearch reclustering at 97% 37957 106 1
OTU vs after mumu cleaning algorithm 37957 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_27Ea_S208
nb_sequences nb_clusters nb_samples
ASV denoising 32105 84 1
OTU after vsearch reclustering at 97% 32105 77 1
OTU vs after mumu cleaning algorithm 32105 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_27Eb_S312
nb_sequences nb_clusters nb_samples
ASV denoising 26940 104 1
OTU after vsearch reclustering at 97% 26940 89 1
OTU vs after mumu cleaning algorithm 26940 89 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_27F_S88
nb_sequences nb_clusters nb_samples
ASV denoising 33313 54 1
OTU after vsearch reclustering at 97% 33313 46 1
OTU vs after mumu cleaning algorithm 33313 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_27Fa_S256
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Fb_S288
nb_sequences nb_clusters nb_samples
ASV denoising 17375 51 1
OTU after vsearch reclustering at 97% 17375 42 1
OTU vs after mumu cleaning algorithm 17375 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_27G_S5
nb_sequences nb_clusters nb_samples
ASV denoising 47979 124 1
OTU after vsearch reclustering at 97% 47979 92 1
OTU vs after mumu cleaning algorithm 47979 92 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_27Ga_S240
nb_sequences nb_clusters nb_samples
ASV denoising 26 1 1
OTU after vsearch reclustering at 97% 26 1 1
OTU vs after mumu cleaning algorithm 26 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Gb_S242
nb_sequences nb_clusters nb_samples
ASV denoising 32556 100 1
OTU after vsearch reclustering at 97% 32556 81 1
OTU vs after mumu cleaning algorithm 32556 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_27H_S46
nb_sequences nb_clusters nb_samples
ASV denoising 43138 111 1
OTU after vsearch reclustering at 97% 43138 82 1
OTU vs after mumu cleaning algorithm 43138 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_27Ha_S287
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27Hb_S280
nb_sequences nb_clusters nb_samples
ASV denoising 1 1 1
OTU after vsearch reclustering at 97% 1 1 1
OTU vs after mumu cleaning algorithm 1 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_27I_S158
nb_sequences nb_clusters nb_samples
ASV denoising 33676 44 1
OTU after vsearch reclustering at 97% 33676 33 1
OTU vs after mumu cleaning algorithm 33676 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_27Ia_S245
nb_sequences nb_clusters nb_samples
ASV denoising 36653 65 1
OTU after vsearch reclustering at 97% 36653 53 1
OTU vs after mumu cleaning algorithm 36653 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_27Ib_S247
nb_sequences nb_clusters nb_samples
ASV denoising 30758 59 1
OTU after vsearch reclustering at 97% 30758 46 1
OTU vs after mumu cleaning algorithm 30758 45 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_28A_S9
nb_sequences nb_clusters nb_samples
ASV denoising 35935 76 1
OTU after vsearch reclustering at 97% 35935 49 1
OTU vs after mumu cleaning algorithm 35935 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_28B_S33
nb_sequences nb_clusters nb_samples
ASV denoising 26035 72 1
OTU after vsearch reclustering at 97% 26035 59 1
OTU vs after mumu cleaning algorithm 26035 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_28C_S31
nb_sequences nb_clusters nb_samples
ASV denoising 22155 45 1
OTU after vsearch reclustering at 97% 22155 35 1
OTU vs after mumu cleaning algorithm 22155 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_29A_S117
nb_sequences nb_clusters nb_samples
ASV denoising 42328 97 1
OTU after vsearch reclustering at 97% 42328 71 1
OTU vs after mumu cleaning algorithm 42328 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_29B_S187
nb_sequences nb_clusters nb_samples
ASV denoising 1033 24 1
OTU after vsearch reclustering at 97% 1033 23 1
OTU vs after mumu cleaning algorithm 1033 22 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_29C_S90
nb_sequences nb_clusters nb_samples
ASV denoising 40604 82 1
OTU after vsearch reclustering at 97% 40604 69 1
OTU vs after mumu cleaning algorithm 40604 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_29D_S71
nb_sequences nb_clusters nb_samples
ASV denoising 23180 89 1
OTU after vsearch reclustering at 97% 23180 61 1
OTU vs after mumu cleaning algorithm 23180 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_29F_S59
nb_sequences nb_clusters nb_samples
ASV denoising 46305 26 1
OTU after vsearch reclustering at 97% 46305 17 1
OTU vs after mumu cleaning algorithm 46305 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_29H1-50_S34
nb_sequences nb_clusters nb_samples
ASV denoising 27242 110 1
OTU after vsearch reclustering at 97% 27242 105 1
OTU vs after mumu cleaning algorithm 27242 94 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_29H1-50-PL1_S3
nb_sequences nb_clusters nb_samples
ASV denoising 33025 80 1
OTU after vsearch reclustering at 97% 33025 61 1
OTU vs after mumu cleaning algorithm 33025 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_29I_S58
nb_sequences nb_clusters nb_samples
ASV denoising 35649 74 1
OTU after vsearch reclustering at 97% 35649 46 1
OTU vs after mumu cleaning algorithm 35649 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_29I1-50_S85
nb_sequences nb_clusters nb_samples
ASV denoising 42520 131 1
OTU after vsearch reclustering at 97% 42520 90 1
OTU vs after mumu cleaning algorithm 42520 88 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_29J_S40
nb_sequences nb_clusters nb_samples
ASV denoising 37596 85 1
OTU after vsearch reclustering at 97% 37596 50 1
OTU vs after mumu cleaning algorithm 37596 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_29K_S175
nb_sequences nb_clusters nb_samples
ASV denoising 41112 113 1
OTU after vsearch reclustering at 97% 41112 77 1
OTU vs after mumu cleaning algorithm 41112 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_29K-PL1_S26
nb_sequences nb_clusters nb_samples
ASV denoising 40677 85 1
OTU after vsearch reclustering at 97% 40677 50 1
OTU vs after mumu cleaning algorithm 40677 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_29L_S122
nb_sequences nb_clusters nb_samples
ASV denoising 46588 66 1
OTU after vsearch reclustering at 97% 46588 57 1
OTU vs after mumu cleaning algorithm 46588 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_31-32A_S155
nb_sequences nb_clusters nb_samples
ASV denoising 34 1 1
OTU after vsearch reclustering at 97% 34 1 1
OTU vs after mumu cleaning algorithm 34 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_31-32A-PL2_S101
nb_sequences nb_clusters nb_samples
ASV denoising 43301 88 1
OTU after vsearch reclustering at 97% 43301 66 1
OTU vs after mumu cleaning algorithm 43301 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_31-32B_S157
nb_sequences nb_clusters nb_samples
ASV denoising 38974 86 1
OTU after vsearch reclustering at 97% 38974 65 1
OTU vs after mumu cleaning algorithm 38974 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_31-32C_S137
nb_sequences nb_clusters nb_samples
ASV denoising 11583 39 1
OTU after vsearch reclustering at 97% 11583 27 1
OTU vs after mumu cleaning algorithm 11583 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_31-32E_S124
nb_sequences nb_clusters nb_samples
ASV denoising 35315 112 1
OTU after vsearch reclustering at 97% 35315 101 1
OTU vs after mumu cleaning algorithm 35315 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_31-32F_S199
nb_sequences nb_clusters nb_samples
ASV denoising 34203 56 1
OTU after vsearch reclustering at 97% 34203 36 1
OTU vs after mumu cleaning algorithm 34203 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_31A_S21
nb_sequences nb_clusters nb_samples
ASV denoising 33488 84 1
OTU after vsearch reclustering at 97% 33488 65 1
OTU vs after mumu cleaning algorithm 33488 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_31B_S79
nb_sequences nb_clusters nb_samples
ASV denoising 45605 38 1
OTU after vsearch reclustering at 97% 45605 34 1
OTU vs after mumu cleaning algorithm 45605 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_31C_S36
nb_sequences nb_clusters nb_samples
ASV denoising 38750 143 1
OTU after vsearch reclustering at 97% 38750 112 1
OTU vs after mumu cleaning algorithm 38750 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_32A_S95
nb_sequences nb_clusters nb_samples
ASV denoising 45186 114 1
OTU after vsearch reclustering at 97% 45186 70 1
OTU vs after mumu cleaning algorithm 45186 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_32B_S39
nb_sequences nb_clusters nb_samples
ASV denoising 627 17 1
OTU after vsearch reclustering at 97% 627 17 1
OTU vs after mumu cleaning algorithm 627 17 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_32C_S23
nb_sequences nb_clusters nb_samples
ASV denoising 56952 52 1
OTU after vsearch reclustering at 97% 56952 30 1
OTU vs after mumu cleaning algorithm 56952 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_33A_S179
nb_sequences nb_clusters nb_samples
ASV denoising 23291 7 1
OTU after vsearch reclustering at 97% 23291 4 1
OTU vs after mumu cleaning algorithm 23291 4 1
OTU vs + mumu + rarefaction by sequencing depth 2000 4 1
samp_33C_S136
nb_sequences nb_clusters nb_samples
ASV denoising 38854 125 1
OTU after vsearch reclustering at 97% 38854 112 1
OTU vs after mumu cleaning algorithm 38854 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_33C-PL2_S108
nb_sequences nb_clusters nb_samples
ASV denoising 20795 48 1
OTU after vsearch reclustering at 97% 20795 39 1
OTU vs after mumu cleaning algorithm 20795 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_35A_S1
nb_sequences nb_clusters nb_samples
ASV denoising 41587 66 1
OTU after vsearch reclustering at 97% 41587 43 1
OTU vs after mumu cleaning algorithm 41587 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_35B_S63
nb_sequences nb_clusters nb_samples
ASV denoising 29803 61 1
OTU after vsearch reclustering at 97% 29803 45 1
OTU vs after mumu cleaning algorithm 29803 45 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_35Ba_S301
nb_sequences nb_clusters nb_samples
ASV denoising 36530 99 1
OTU after vsearch reclustering at 97% 36530 82 1
OTU vs after mumu cleaning algorithm 36530 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_35Bb_S297
nb_sequences nb_clusters nb_samples
ASV denoising 35213 71 1
OTU after vsearch reclustering at 97% 35213 52 1
OTU vs after mumu cleaning algorithm 35213 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_35C_S4
nb_sequences nb_clusters nb_samples
ASV denoising 1673 15 1
OTU after vsearch reclustering at 97% 1673 14 1
OTU vs after mumu cleaning algorithm 1673 14 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_35Ca_S302
nb_sequences nb_clusters nb_samples
ASV denoising 51 1 1
OTU after vsearch reclustering at 97% 51 1 1
OTU vs after mumu cleaning algorithm 51 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_35Cb_S275
nb_sequences nb_clusters nb_samples
ASV denoising 20325 107 1
OTU after vsearch reclustering at 97% 20325 98 1
OTU vs after mumu cleaning algorithm 20325 98 1
OTU vs + mumu + rarefaction by sequencing depth 2000 86 1
samp_35D_S165
nb_sequences nb_clusters nb_samples
ASV denoising 35959 86 1
OTU after vsearch reclustering at 97% 35959 52 1
OTU vs after mumu cleaning algorithm 35959 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_35Da_S227
nb_sequences nb_clusters nb_samples
ASV denoising 25855 71 1
OTU after vsearch reclustering at 97% 25855 47 1
OTU vs after mumu cleaning algorithm 25855 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_35Db_S315
nb_sequences nb_clusters nb_samples
ASV denoising 28317 66 1
OTU after vsearch reclustering at 97% 28317 40 1
OTU vs after mumu cleaning algorithm 28317 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_35Ea_S228
nb_sequences nb_clusters nb_samples
ASV denoising 20317 56 1
OTU after vsearch reclustering at 97% 20317 40 1
OTU vs after mumu cleaning algorithm 20317 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_35Eb_S216
nb_sequences nb_clusters nb_samples
ASV denoising 27770 62 1
OTU after vsearch reclustering at 97% 27770 38 1
OTU vs after mumu cleaning algorithm 27770 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_35Fa_S250
nb_sequences nb_clusters nb_samples
ASV denoising 39190 38 1
OTU after vsearch reclustering at 97% 39190 29 1
OTU vs after mumu cleaning algorithm 39190 29 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_35Fb_S244
nb_sequences nb_clusters nb_samples
ASV denoising 44759 49 1
OTU after vsearch reclustering at 97% 44759 32 1
OTU vs after mumu cleaning algorithm 44759 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_35G_S14
nb_sequences nb_clusters nb_samples
ASV denoising 39031 55 1
OTU after vsearch reclustering at 97% 39031 35 1
OTU vs after mumu cleaning algorithm 39031 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_35Ga_S314
nb_sequences nb_clusters nb_samples
ASV denoising 31386 64 1
OTU after vsearch reclustering at 97% 31386 57 1
OTU vs after mumu cleaning algorithm 31386 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_35Gb_S262
nb_sequences nb_clusters nb_samples
ASV denoising 32622 66 1
OTU after vsearch reclustering at 97% 32622 51 1
OTU vs after mumu cleaning algorithm 32622 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_35H_S162
nb_sequences nb_clusters nb_samples
ASV denoising 43714 59 1
OTU after vsearch reclustering at 97% 43714 46 1
OTU vs after mumu cleaning algorithm 43714 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_35Ha_S273
nb_sequences nb_clusters nb_samples
ASV denoising 27159 57 1
OTU after vsearch reclustering at 97% 27159 48 1
OTU vs after mumu cleaning algorithm 27159 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_35Hb_S248
nb_sequences nb_clusters nb_samples
ASV denoising 34068 71 1
OTU after vsearch reclustering at 97% 34068 50 1
OTU vs after mumu cleaning algorithm 34068 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_35Ia_S274
nb_sequences nb_clusters nb_samples
ASV denoising 28834 46 1
OTU after vsearch reclustering at 97% 28834 36 1
OTU vs after mumu cleaning algorithm 28834 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_35Ib_S234
nb_sequences nb_clusters nb_samples
ASV denoising 31094 32 1
OTU after vsearch reclustering at 97% 31094 23 1
OTU vs after mumu cleaning algorithm 31094 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 19 1
samp_36A_S10
nb_sequences nb_clusters nb_samples
ASV denoising 48553 101 1
OTU after vsearch reclustering at 97% 48553 59 1
OTU vs after mumu cleaning algorithm 48553 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_36B_S28
nb_sequences nb_clusters nb_samples
ASV denoising 35133 65 1
OTU after vsearch reclustering at 97% 35133 54 1
OTU vs after mumu cleaning algorithm 35133 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_36B1-50_S41
nb_sequences nb_clusters nb_samples
ASV denoising 40872 82 1
OTU after vsearch reclustering at 97% 40872 61 1
OTU vs after mumu cleaning algorithm 40872 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_36C_S11
nb_sequences nb_clusters nb_samples
ASV denoising 179 9 1
OTU after vsearch reclustering at 97% 179 9 1
OTU vs after mumu cleaning algorithm 179 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_36D_S16
nb_sequences nb_clusters nb_samples
ASV denoising 36863 117 1
OTU after vsearch reclustering at 97% 36863 105 1
OTU vs after mumu cleaning algorithm 36863 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_36E_S91
nb_sequences nb_clusters nb_samples
ASV denoising 78 2 1
OTU after vsearch reclustering at 97% 78 2 1
OTU vs after mumu cleaning algorithm 78 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_36F_S75
nb_sequences nb_clusters nb_samples
ASV denoising 314 6 1
OTU after vsearch reclustering at 97% 314 5 1
OTU vs after mumu cleaning algorithm 314 5 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_37B_S150
nb_sequences nb_clusters nb_samples
ASV denoising 23763 97 1
OTU after vsearch reclustering at 97% 23763 73 1
OTU vs after mumu cleaning algorithm 23763 73 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_37C_S125
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_37D_S100
nb_sequences nb_clusters nb_samples
ASV denoising 27320 100 1
OTU after vsearch reclustering at 97% 27320 80 1
OTU vs after mumu cleaning algorithm 27320 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_38A_S70
nb_sequences nb_clusters nb_samples
ASV denoising 47864 118 1
OTU after vsearch reclustering at 97% 47864 89 1
OTU vs after mumu cleaning algorithm 47864 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_38B_S18
nb_sequences nb_clusters nb_samples
ASV denoising 38946 72 1
OTU after vsearch reclustering at 97% 38946 52 1
OTU vs after mumu cleaning algorithm 38946 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_38C_S152
nb_sequences nb_clusters nb_samples
ASV denoising 26201 155 1
OTU after vsearch reclustering at 97% 26201 146 1
OTU vs after mumu cleaning algorithm 26201 143 1
OTU vs + mumu + rarefaction by sequencing depth 2000 118 1
samp_38D_S13
nb_sequences nb_clusters nb_samples
ASV denoising 36873 123 1
OTU after vsearch reclustering at 97% 36873 103 1
OTU vs after mumu cleaning algorithm 36873 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 85 1
samp_39A_S51
nb_sequences nb_clusters nb_samples
ASV denoising 33352 50 1
OTU after vsearch reclustering at 97% 33352 39 1
OTU vs after mumu cleaning algorithm 33352 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_39B_S42
nb_sequences nb_clusters nb_samples
ASV denoising 67 2 1
OTU after vsearch reclustering at 97% 67 2 1
OTU vs after mumu cleaning algorithm 67 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_39C_S99
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_40A_S61
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_40B_S106
nb_sequences nb_clusters nb_samples
ASV denoising 39358 128 1
OTU after vsearch reclustering at 97% 39358 111 1
OTU vs after mumu cleaning algorithm 39358 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_40Bbis_S55
nb_sequences nb_clusters nb_samples
ASV denoising 20187 83 1
OTU after vsearch reclustering at 97% 20187 76 1
OTU vs after mumu cleaning algorithm 20187 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 70 1
samp_40G_S29
nb_sequences nb_clusters nb_samples
ASV denoising 98 2 1
OTU after vsearch reclustering at 97% 98 2 1
OTU vs after mumu cleaning algorithm 98 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_41A_S22
nb_sequences nb_clusters nb_samples
ASV denoising 28674 63 1
OTU after vsearch reclustering at 97% 28674 49 1
OTU vs after mumu cleaning algorithm 28674 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_41C_S92
nb_sequences nb_clusters nb_samples
ASV denoising 19356 101 1
OTU after vsearch reclustering at 97% 19356 92 1
OTU vs after mumu cleaning algorithm 19356 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_42A_S147
nb_sequences nb_clusters nb_samples
ASV denoising 40772 88 1
OTU after vsearch reclustering at 97% 40772 43 1
OTU vs after mumu cleaning algorithm 40772 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_42Aa_S309
nb_sequences nb_clusters nb_samples
ASV denoising 425 15 1
OTU after vsearch reclustering at 97% 425 15 1
OTU vs after mumu cleaning algorithm 425 15 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Aa-PL3_S226
nb_sequences nb_clusters nb_samples
ASV denoising 310 13 1
OTU after vsearch reclustering at 97% 310 13 1
OTU vs after mumu cleaning algorithm 310 13 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42B_S161
nb_sequences nb_clusters nb_samples
ASV denoising 1765 15 1
OTU after vsearch reclustering at 97% 1765 15 1
OTU vs after mumu cleaning algorithm 1765 15 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Ba_S270
nb_sequences nb_clusters nb_samples
ASV denoising 372 8 1
OTU after vsearch reclustering at 97% 372 8 1
OTU vs after mumu cleaning algorithm 372 8 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Bb_S305
nb_sequences nb_clusters nb_samples
ASV denoising 38308 55 1
OTU after vsearch reclustering at 97% 38308 41 1
OTU vs after mumu cleaning algorithm 38308 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_42C_S205
nb_sequences nb_clusters nb_samples
ASV denoising 510 9 1
OTU after vsearch reclustering at 97% 510 9 1
OTU vs after mumu cleaning algorithm 510 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Ca_S260
nb_sequences nb_clusters nb_samples
ASV denoising 48 1 1
OTU after vsearch reclustering at 97% 48 1 1
OTU vs after mumu cleaning algorithm 48 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42D_S127
nb_sequences nb_clusters nb_samples
ASV denoising 35381 82 1
OTU after vsearch reclustering at 97% 35381 66 1
OTU vs after mumu cleaning algorithm 35381 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_42Da_S307
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_42Db_S255
nb_sequences nb_clusters nb_samples
ASV denoising 36406 132 1
OTU after vsearch reclustering at 97% 36406 112 1
OTU vs after mumu cleaning algorithm 36406 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_42E_S171
nb_sequences nb_clusters nb_samples
ASV denoising 31804 86 1
OTU after vsearch reclustering at 97% 31804 63 1
OTU vs after mumu cleaning algorithm 31804 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_42Ea_S308
nb_sequences nb_clusters nb_samples
ASV denoising 7329 83 1
OTU after vsearch reclustering at 97% 7329 82 1
OTU vs after mumu cleaning algorithm 7329 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_42Eb_S263
nb_sequences nb_clusters nb_samples
ASV denoising 29413 149 1
OTU after vsearch reclustering at 97% 29413 130 1
OTU vs after mumu cleaning algorithm 29413 128 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_42F_S129
nb_sequences nb_clusters nb_samples
ASV denoising 37829 94 1
OTU after vsearch reclustering at 97% 37829 88 1
OTU vs after mumu cleaning algorithm 37829 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 69 1
samp_42Fa_S266
nb_sequences nb_clusters nb_samples
ASV denoising 32192 112 1
OTU after vsearch reclustering at 97% 32192 106 1
OTU vs after mumu cleaning algorithm 32192 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_42Fb-PL3_S264
nb_sequences nb_clusters nb_samples
ASV denoising 25379 65 1
OTU after vsearch reclustering at 97% 25379 61 1
OTU vs after mumu cleaning algorithm 25379 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_42G_S107
nb_sequences nb_clusters nb_samples
ASV denoising 21661 40 1
OTU after vsearch reclustering at 97% 21661 33 1
OTU vs after mumu cleaning algorithm 21661 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_42Ga2_S254
nb_sequences nb_clusters nb_samples
ASV denoising 28887 119 1
OTU after vsearch reclustering at 97% 28887 107 1
OTU vs after mumu cleaning algorithm 28887 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_42Gb_S209
nb_sequences nb_clusters nb_samples
ASV denoising 9891 58 1
OTU after vsearch reclustering at 97% 9891 53 1
OTU vs after mumu cleaning algorithm 9891 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_42H_S186
nb_sequences nb_clusters nb_samples
ASV denoising 24791 61 1
OTU after vsearch reclustering at 97% 24791 51 1
OTU vs after mumu cleaning algorithm 24791 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_42Ha_S286
nb_sequences nb_clusters nb_samples
ASV denoising 26588 102 1
OTU after vsearch reclustering at 97% 26588 92 1
OTU vs after mumu cleaning algorithm 26588 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_42Hb_S268
nb_sequences nb_clusters nb_samples
ASV denoising 20124 97 1
OTU after vsearch reclustering at 97% 20124 91 1
OTU vs after mumu cleaning algorithm 20124 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_42I_S169
nb_sequences nb_clusters nb_samples
ASV denoising 40911 58 1
OTU after vsearch reclustering at 97% 40911 40 1
OTU vs after mumu cleaning algorithm 40911 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_42Ia_S223
nb_sequences nb_clusters nb_samples
ASV denoising 36041 44 1
OTU after vsearch reclustering at 97% 36041 30 1
OTU vs after mumu cleaning algorithm 36041 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_42Ib_S317
nb_sequences nb_clusters nb_samples
ASV denoising 34484 56 1
OTU after vsearch reclustering at 97% 34484 45 1
OTU vs after mumu cleaning algorithm 34484 45 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_43A_S64
nb_sequences nb_clusters nb_samples
ASV denoising 147 4 1
OTU after vsearch reclustering at 97% 147 4 1
OTU vs after mumu cleaning algorithm 147 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43C_S149
nb_sequences nb_clusters nb_samples
ASV denoising 190 3 1
OTU after vsearch reclustering at 97% 190 3 1
OTU vs after mumu cleaning algorithm 190 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43D_S69
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_43E_S142
nb_sequences nb_clusters nb_samples
ASV denoising 33326 183 1
OTU after vsearch reclustering at 97% 33326 163 1
OTU vs after mumu cleaning algorithm 33326 154 1
OTU vs + mumu + rarefaction by sequencing depth 2000 130 1
samp_43F_S177
nb_sequences nb_clusters nb_samples
ASV denoising 405 4 1
OTU after vsearch reclustering at 97% 405 4 1
OTU vs after mumu cleaning algorithm 405 4 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_44A_S193
nb_sequences nb_clusters nb_samples
ASV denoising 34457 80 1
OTU after vsearch reclustering at 97% 34457 58 1
OTU vs after mumu cleaning algorithm 34457 55 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_44C_S164
nb_sequences nb_clusters nb_samples
ASV denoising 44924 42 1
OTU after vsearch reclustering at 97% 44924 34 1
OTU vs after mumu cleaning algorithm 44924 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_45_S110
nb_sequences nb_clusters nb_samples
ASV denoising 27005 129 1
OTU after vsearch reclustering at 97% 27005 116 1
OTU vs after mumu cleaning algorithm 27005 107 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_46F_S202
nb_sequences nb_clusters nb_samples
ASV denoising 26758 78 1
OTU after vsearch reclustering at 97% 26758 50 1
OTU vs after mumu cleaning algorithm 26758 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_47A1-50_S20
nb_sequences nb_clusters nb_samples
ASV denoising 34130 79 1
OTU after vsearch reclustering at 97% 34130 65 1
OTU vs after mumu cleaning algorithm 34130 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_47D_S211
nb_sequences nb_clusters nb_samples
ASV denoising 30757 96 1
OTU after vsearch reclustering at 97% 30757 76 1
OTU vs after mumu cleaning algorithm 30757 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 69 1
samp_47E_S218
nb_sequences nb_clusters nb_samples
ASV denoising 35102 96 1
OTU after vsearch reclustering at 97% 35102 76 1
OTU vs after mumu cleaning algorithm 35102 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_47F_S210
nb_sequences nb_clusters nb_samples
ASV denoising 22005 62 1
OTU after vsearch reclustering at 97% 22005 50 1
OTU vs after mumu cleaning algorithm 22005 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_47F-PL1_S6
nb_sequences nb_clusters nb_samples
ASV denoising 31344 96 1
OTU after vsearch reclustering at 97% 31344 75 1
OTU vs after mumu cleaning algorithm 31344 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_48a_S231
nb_sequences nb_clusters nb_samples
ASV denoising 41121 60 1
OTU after vsearch reclustering at 97% 41121 32 1
OTU vs after mumu cleaning algorithm 41121 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_48B_S215
nb_sequences nb_clusters nb_samples
ASV denoising 31011 81 1
OTU after vsearch reclustering at 97% 31011 56 1
OTU vs after mumu cleaning algorithm 31011 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 51 1
samp_48C_S204
nb_sequences nb_clusters nb_samples
ASV denoising 34555 81 1
OTU after vsearch reclustering at 97% 34555 59 1
OTU vs after mumu cleaning algorithm 34555 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_48D_S201
nb_sequences nb_clusters nb_samples
ASV denoising 15814 58 1
OTU after vsearch reclustering at 97% 15814 54 1
OTU vs after mumu cleaning algorithm 15814 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_48E_S206
nb_sequences nb_clusters nb_samples
ASV denoising 26927 51 1
OTU after vsearch reclustering at 97% 26927 39 1
OTU vs after mumu cleaning algorithm 26927 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_48F_S203
nb_sequences nb_clusters nb_samples
ASV denoising 29682 77 1
OTU after vsearch reclustering at 97% 29682 57 1
OTU vs after mumu cleaning algorithm 29682 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_49A_S78
nb_sequences nb_clusters nb_samples
ASV denoising 38500 123 1
OTU after vsearch reclustering at 97% 38500 98 1
OTU vs after mumu cleaning algorithm 38500 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 82 1
samp_49B_S2
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49B1-50_S27
nb_sequences nb_clusters nb_samples
ASV denoising 39646 133 1
OTU after vsearch reclustering at 97% 39646 100 1
OTU vs after mumu cleaning algorithm 39646 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_49C_S159
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49D_S86
nb_sequences nb_clusters nb_samples
ASV denoising 559 6 1
OTU after vsearch reclustering at 97% 559 5 1
OTU vs after mumu cleaning algorithm 559 5 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_49E_S72
nb_sequences nb_clusters nb_samples
ASV denoising 43668 63 1
OTU after vsearch reclustering at 97% 43668 44 1
OTU vs after mumu cleaning algorithm 43668 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_49F_S120
nb_sequences nb_clusters nb_samples
ASV denoising 28547 113 1
OTU after vsearch reclustering at 97% 28547 95 1
OTU vs after mumu cleaning algorithm 28547 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_52C_S57
nb_sequences nb_clusters nb_samples
ASV denoising 7786 50 1
OTU after vsearch reclustering at 97% 7786 47 1
OTU vs after mumu cleaning algorithm 7786 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 44 1
samp_52D_S56
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_57S_S43
nb_sequences nb_clusters nb_samples
ASV denoising 38415 96 1
OTU after vsearch reclustering at 97% 38415 81 1
OTU vs after mumu cleaning algorithm 38415 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_B1_S30
nb_sequences nb_clusters nb_samples
ASV denoising 40928 68 1
OTU after vsearch reclustering at 97% 40928 56 1
OTU vs after mumu cleaning algorithm 40928 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_B3_S25
nb_sequences nb_clusters nb_samples
ASV denoising 37572 28 1
OTU after vsearch reclustering at 97% 37572 11 1
OTU vs after mumu cleaning algorithm 37572 11 1
OTU vs + mumu + rarefaction by sequencing depth 2000 11 1
samp_B4_S37
nb_sequences nb_clusters nb_samples
ASV denoising 30591 22 1
OTU after vsearch reclustering at 97% 30591 13 1
OTU vs after mumu cleaning algorithm 30591 13 1
OTU vs + mumu + rarefaction by sequencing depth 2000 13 1
samp_BI_S320
nb_sequences nb_clusters nb_samples
ASV denoising 31827 71 1
OTU after vsearch reclustering at 97% 31827 70 1
OTU vs after mumu cleaning algorithm 31827 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_Blanc_S212
nb_sequences nb_clusters nb_samples
ASV denoising 28671 11 1
OTU after vsearch reclustering at 97% 28671 9 1
OTU vs after mumu cleaning algorithm 28671 9 1
OTU vs + mumu + rarefaction by sequencing depth 2000 9 1
samp_Blnc35I-PL2_S184
nb_sequences nb_clusters nb_samples
ASV denoising 29268 10 1
OTU after vsearch reclustering at 97% 29268 5 1
OTU vs after mumu cleaning algorithm 29268 5 1
OTU vs + mumu + rarefaction by sequencing depth 2000 5 1
samp_GENSEQ1_S96
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_GENSEQ3_S281
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_GENSEQ5_S375
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_inconnus_S322
nb_sequences nb_clusters nb_samples
ASV denoising 393 1 1
OTU after vsearch reclustering at 97% 393 1 1
OTU vs after mumu cleaning algorithm 393 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL1-H12-35F_S324
nb_sequences nb_clusters nb_samples
ASV denoising 37976 57 1
OTU after vsearch reclustering at 97% 37976 40 1
OTU vs after mumu cleaning algorithm 37976 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_PL2-A1-33B_S325
nb_sequences nb_clusters nb_samples
ASV denoising 20571 83 1
OTU after vsearch reclustering at 97% 20571 77 1
OTU vs after mumu cleaning algorithm 20571 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_PL3-A12-35Aa_S326
nb_sequences nb_clusters nb_samples
ASV denoising 20729 63 1
OTU after vsearch reclustering at 97% 20729 59 1
OTU vs after mumu cleaning algorithm 20729 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_PL5-004a_S327
nb_sequences nb_clusters nb_samples
ASV denoising 17866 83 1
OTU after vsearch reclustering at 97% 17866 68 1
OTU vs after mumu cleaning algorithm 17866 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_PL5-004Ab_S328
nb_sequences nb_clusters nb_samples
ASV denoising 25067 111 1
OTU after vsearch reclustering at 97% 25067 89 1
OTU vs after mumu cleaning algorithm 25067 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_PL5-004Ba_S329
nb_sequences nb_clusters nb_samples
ASV denoising 24545 63 1
OTU after vsearch reclustering at 97% 24545 42 1
OTU vs after mumu cleaning algorithm 24545 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_PL5-004Cb_S332
nb_sequences nb_clusters nb_samples
ASV denoising 10963 44 1
OTU after vsearch reclustering at 97% 10963 39 1
OTU vs after mumu cleaning algorithm 10963 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 37 1
samp_PL5-005Aa_S333
nb_sequences nb_clusters nb_samples
ASV denoising 17343 95 1
OTU after vsearch reclustering at 97% 17343 85 1
OTU vs after mumu cleaning algorithm 17343 83 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_PL5-005Ba_S335
nb_sequences nb_clusters nb_samples
ASV denoising 33006 84 1
OTU after vsearch reclustering at 97% 33006 68 1
OTU vs after mumu cleaning algorithm 33006 68 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_PL5-005Bb_S334
nb_sequences nb_clusters nb_samples
ASV denoising 20 1 1
OTU after vsearch reclustering at 97% 20 1 1
OTU vs after mumu cleaning algorithm 20 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL5-005Ca_S336
nb_sequences nb_clusters nb_samples
ASV denoising 29219 99 1
OTU after vsearch reclustering at 97% 29219 94 1
OTU vs after mumu cleaning algorithm 29219 93 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_PL5-005Cb_S337
nb_sequences nb_clusters nb_samples
ASV denoising 28152 131 1
OTU after vsearch reclustering at 97% 28152 113 1
OTU vs after mumu cleaning algorithm 28152 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_PL5-006Aa_S338
nb_sequences nb_clusters nb_samples
ASV denoising 36650 143 1
OTU after vsearch reclustering at 97% 36650 122 1
OTU vs after mumu cleaning algorithm 36650 121 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_PL5-006Ab_S339
nb_sequences nb_clusters nb_samples
ASV denoising 20337 107 1
OTU after vsearch reclustering at 97% 20337 97 1
OTU vs after mumu cleaning algorithm 20337 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 88 1
samp_PL5-006Ba_S340
nb_sequences nb_clusters nb_samples
ASV denoising 27803 120 1
OTU after vsearch reclustering at 97% 27803 105 1
OTU vs after mumu cleaning algorithm 27803 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 91 1
samp_PL5-006Bb_S341
nb_sequences nb_clusters nb_samples
ASV denoising 10514 88 1
OTU after vsearch reclustering at 97% 10514 81 1
OTU vs after mumu cleaning algorithm 10514 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_PL5-006Ca_S342
nb_sequences nb_clusters nb_samples
ASV denoising 25909 115 1
OTU after vsearch reclustering at 97% 25909 101 1
OTU vs after mumu cleaning algorithm 25909 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_PL5-006Cb_S343
nb_sequences nb_clusters nb_samples
ASV denoising 28260 112 1
OTU after vsearch reclustering at 97% 28260 102 1
OTU vs after mumu cleaning algorithm 28260 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 84 1
samp_PL5-024A_S348
nb_sequences nb_clusters nb_samples
ASV denoising 36413 98 1
OTU after vsearch reclustering at 97% 36413 80 1
OTU vs after mumu cleaning algorithm 36413 80 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_PL5-024B_S349
nb_sequences nb_clusters nb_samples
ASV denoising 21441 117 1
OTU after vsearch reclustering at 97% 21441 100 1
OTU vs after mumu cleaning algorithm 21441 100 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_PL5-024D_S351
nb_sequences nb_clusters nb_samples
ASV denoising 46337 137 1
OTU after vsearch reclustering at 97% 46337 107 1
OTU vs after mumu cleaning algorithm 46337 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_PL5-024E_S352
nb_sequences nb_clusters nb_samples
ASV denoising 32270 136 1
OTU after vsearch reclustering at 97% 32270 118 1
OTU vs after mumu cleaning algorithm 32270 117 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_PL5-21Aa_S344
nb_sequences nb_clusters nb_samples
ASV denoising 25882 123 1
OTU after vsearch reclustering at 97% 25882 112 1
OTU vs after mumu cleaning algorithm 25882 111 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_PL5-21Ab_S345
nb_sequences nb_clusters nb_samples
ASV denoising 29991 86 1
OTU after vsearch reclustering at 97% 29991 62 1
OTU vs after mumu cleaning algorithm 29991 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_PL5-21Ba_S346
nb_sequences nb_clusters nb_samples
ASV denoising 26238 67 1
OTU after vsearch reclustering at 97% 26238 52 1
OTU vs after mumu cleaning algorithm 26238 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_PL5-21Bb_S347
nb_sequences nb_clusters nb_samples
ASV denoising 35125 81 1
OTU after vsearch reclustering at 97% 35125 65 1
OTU vs after mumu cleaning algorithm 35125 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_PL5-24C_S350
nb_sequences nb_clusters nb_samples
ASV denoising 33655 94 1
OTU after vsearch reclustering at 97% 33655 79 1
OTU vs after mumu cleaning algorithm 33655 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_PL5-24F_S353
nb_sequences nb_clusters nb_samples
ASV denoising 31490 103 1
OTU after vsearch reclustering at 97% 31490 80 1
OTU vs after mumu cleaning algorithm 31490 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_PL5-24G_S354
nb_sequences nb_clusters nb_samples
ASV denoising 33105 87 1
OTU after vsearch reclustering at 97% 33105 66 1
OTU vs after mumu cleaning algorithm 33105 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_PL5-24H_S355
nb_sequences nb_clusters nb_samples
ASV denoising 26770 106 1
OTU after vsearch reclustering at 97% 26770 100 1
OTU vs after mumu cleaning algorithm 26770 99 1
OTU vs + mumu + rarefaction by sequencing depth 2000 88 1
samp_PL5-24J_S356
nb_sequences nb_clusters nb_samples
ASV denoising 22145 39 1
OTU after vsearch reclustering at 97% 22145 35 1
OTU vs after mumu cleaning algorithm 22145 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_PL5-35I_S357
nb_sequences nb_clusters nb_samples
ASV denoising 27193 164 1
OTU after vsearch reclustering at 97% 27193 148 1
OTU vs after mumu cleaning algorithm 27193 144 1
OTU vs + mumu + rarefaction by sequencing depth 2000 126 1
samp_PL5-36A_S358
nb_sequences nb_clusters nb_samples
ASV denoising 40868 55 1
OTU after vsearch reclustering at 97% 40868 38 1
OTU vs after mumu cleaning algorithm 40868 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_PL5-42E_S359
nb_sequences nb_clusters nb_samples
ASV denoising 28300 99 1
OTU after vsearch reclustering at 97% 28300 67 1
OTU vs after mumu cleaning algorithm 28300 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_PL5-43B_S360
nb_sequences nb_clusters nb_samples
ASV denoising 28161 139 1
OTU after vsearch reclustering at 97% 28161 117 1
OTU vs after mumu cleaning algorithm 28161 114 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_PL5-44B_S361
nb_sequences nb_clusters nb_samples
ASV denoising 35331 107 1
OTU after vsearch reclustering at 97% 35331 99 1
OTU vs after mumu cleaning algorithm 35331 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_PL5-46A_S362
nb_sequences nb_clusters nb_samples
ASV denoising 32906 125 1
OTU after vsearch reclustering at 97% 32906 115 1
OTU vs after mumu cleaning algorithm 32906 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 91 1
samp_PL5-46B_S363
nb_sequences nb_clusters nb_samples
ASV denoising 27790 64 1
OTU after vsearch reclustering at 97% 27790 50 1
OTU vs after mumu cleaning algorithm 27790 50 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_PL5-46D_S365
nb_sequences nb_clusters nb_samples
ASV denoising 30298 57 1
OTU after vsearch reclustering at 97% 30298 34 1
OTU vs after mumu cleaning algorithm 30298 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_PL5-46E_S366
nb_sequences nb_clusters nb_samples
ASV denoising 37112 68 1
OTU after vsearch reclustering at 97% 37112 48 1
OTU vs after mumu cleaning algorithm 37112 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_PL5-47A_S367
nb_sequences nb_clusters nb_samples
ASV denoising 32828 103 1
OTU after vsearch reclustering at 97% 32828 91 1
OTU vs after mumu cleaning algorithm 32828 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_PL5-47B_S368
nb_sequences nb_clusters nb_samples
ASV denoising 26173 70 1
OTU after vsearch reclustering at 97% 26173 48 1
OTU vs after mumu cleaning algorithm 26173 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_PL5-47C_S369
nb_sequences nb_clusters nb_samples
ASV denoising 19259 51 1
OTU after vsearch reclustering at 97% 19259 44 1
OTU vs after mumu cleaning algorithm 19259 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_PL5-50_S370
nb_sequences nb_clusters nb_samples
ASV denoising 27725 78 1
OTU after vsearch reclustering at 97% 27725 73 1
OTU vs after mumu cleaning algorithm 27725 72 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_PL5-53_S371
nb_sequences nb_clusters nb_samples
ASV denoising 16900 66 1
OTU after vsearch reclustering at 97% 16900 59 1
OTU vs after mumu cleaning algorithm 16900 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 53 1
samp_PL5-eau_S374
nb_sequences nb_clusters nb_samples
ASV denoising 0 10154 1
OTU after vsearch reclustering at 97% 0 4483 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PL5-ENC024A_S373
nb_sequences nb_clusters nb_samples
ASV denoising 31599 152 1
OTU after vsearch reclustering at 97% 31599 126 1
OTU vs after mumu cleaning algorithm 31599 124 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_PL5-ENC024C_S372
nb_sequences nb_clusters nb_samples
ASV denoising 19447 133 1
OTU after vsearch reclustering at 97% 19447 125 1
OTU vs after mumu cleaning algorithm 19447 108 1
OTU vs + mumu + rarefaction by sequencing depth 2000 98 1

Make krona html files

Code 
krona(
  clean_pq(d_pq, simplify_taxo = TRUE),
  file = here::here("data/data_final/krona_nb_seq.html")
)
Code 
krona(
  clean_pq(d_pq, simplify_taxo = TRUE),
  nb_seq = FALSE,
  file =  here::here("data/data_final/krona_nb_taxa.html")
)

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data/data_final/information_run.txt .

Code 
sessionInfo()
#> R version 4.5.1 (2025-06-13)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Kali GNU/Linux Rolling
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.29.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
#>  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
#>  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Europe/Paris
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices datasets  utils     methods   base     
#> 
#> other attached packages:
#> [1] MiscMetabar_0.14.4 purrr_1.2.0        dplyr_1.1.4        dada2_1.38.0      
#> [5] Rcpp_1.1.0         ggplot2_4.0.1      phyloseq_1.54.0    targets_1.11.4    
#> [9] knitr_1.50        
#> 
#> loaded via a namespace (and not attached):
#>   [1] greenAlgoR_0.1.2            bitops_1.0-9               
#>   [3] deldir_2.0-4                permute_0.9-8              
#>   [5] rlang_1.1.6                 magrittr_2.0.4             
#>   [7] ade4_1.7-23                 matrixStats_1.5.0          
#>   [9] compiler_4.5.1              mgcv_1.9-4                 
#>  [11] png_0.1-8                   callr_3.7.6                
#>  [13] vctrs_0.6.5                 reshape2_1.4.5             
#>  [15] autometric_0.1.2            stringr_1.6.0              
#>  [17] pwalign_1.6.0               pkgconfig_2.0.3            
#>  [19] crayon_1.5.3                fastmap_1.2.0              
#>  [21] backports_1.5.0             XVector_0.50.0             
#>  [23] labeling_0.4.3              Rsamtools_2.26.0           
#>  [25] rmarkdown_2.30              ps_1.9.1                   
#>  [27] xfun_0.54                   cachem_1.1.0               
#>  [29] cigarillo_1.0.0             jsonlite_2.0.0             
#>  [31] biomformat_1.38.0           rhdf5filters_1.22.0        
#>  [33] DelayedArray_0.36.0         Rhdf5lib_1.32.0            
#>  [35] BiocParallel_1.44.0         jpeg_0.1-11                
#>  [37] parallel_4.5.1              prettyunits_1.2.0          
#>  [39] cluster_2.1.8.1             R6_2.6.1                   
#>  [41] bslib_0.9.0                 stringi_1.8.7              
#>  [43] RColorBrewer_1.1-3          benchmarkme_1.0.8          
#>  [45] jquerylib_0.1.4             GenomicRanges_1.62.0       
#>  [47] Seqinfo_1.0.0               SummarizedExperiment_1.40.0
#>  [49] iterators_1.0.14            IRanges_2.44.0             
#>  [51] Matrix_1.7-4                splines_4.5.1              
#>  [53] igraph_2.2.1                tidyselect_1.2.1           
#>  [55] rstudioapi_0.17.1           abind_1.4-8                
#>  [57] yaml_2.3.10                 vegan_2.7-2                
#>  [59] doParallel_1.0.17           codetools_0.2-20           
#>  [61] hwriter_1.3.2.1             processx_3.8.6             
#>  [63] lattice_0.22-7              tibble_3.3.0               
#>  [65] plyr_1.8.9                  Biobase_2.70.0             
#>  [67] withr_3.0.2                 ShortRead_1.68.0           
#>  [69] S7_0.2.1                    benchmarkmeData_1.0.4      
#>  [71] evaluate_1.0.5              survival_3.8-3             
#>  [73] RcppParallel_5.1.11-1       Biostrings_2.78.0          
#>  [75] pillar_1.11.1               BiocManager_1.30.27        
#>  [77] MatrixGenerics_1.22.0       DT_0.34.0                  
#>  [79] renv_1.0.11                 foreach_1.5.2              
#>  [81] stats4_4.5.1                generics_0.1.4             
#>  [83] rprojroot_2.1.1             S4Vectors_0.48.0           
#>  [85] scales_1.4.0                base64url_1.4              
#>  [87] glue_1.8.0                  tools_4.5.1                
#>  [89] interp_1.1-6                data.table_1.17.8          
#>  [91] GenomicAlignments_1.46.0    visNetwork_2.1.4           
#>  [93] rhdf5_2.54.0                grid_4.5.1                 
#>  [95] ape_5.8-1                   crosstalk_1.2.2            
#>  [97] latticeExtra_0.6-31         nlme_3.1-168               
#>  [99] cli_3.6.5                   viridisLite_0.4.2          
#> [101] S4Arrays_1.10.0             gtable_0.3.6               
#> [103] sass_0.4.10                 digest_0.6.39              
#> [105] BiocGenerics_0.56.0         SparseArray_1.10.3         
#> [107] htmlwidgets_1.6.4           farver_2.1.2               
#> [109] htmltools_0.5.8.1           multtest_2.66.0            
#> [111] lifecycle_1.0.4             httr_1.4.7                 
#> [113] here_1.0.2                  secretbase_1.0.5           
#> [115] MASS_7.3-65

Citation

BibTeX citation:
@online{taudière2025,
  author = {Taudière, Adrien},
  title = {Bioinformatics Pipeline Summary},
  date = {2025-12-01},
  langid = {en}
}
For attribution, please cite this work as:
Taudière, Adrien. 2025. “Bioinformatics Pipeline Summary.” December 1, 2025.

This document was made by the Adrien Taudière, with multiple inspirations from the Lumo quarto template.